IHaskell fails to install to Jupyter Kernel

I'm on Arch Linux and I installed IHaskell from this package on the AUR. https://aur.archlinux.org/packages/ihaskell-git/
I get this error output when I try to install the Jupiter Kernel:
[alan@vbox ~]$ ihaskell install
ihaskell:
Ran commands:
which jupyter
which jupyter
/usr/bin/jupyter --version
which /usr/bin/jupyter
which ihaskell
withTmpDir
rm -f /tmp/tmpThreadId41804289383846930886
mkdir /tmp/tmpThreadId41804289383846930886
mkdir -p /tmp/tmpThreadId41804289383846930886/haskell
writefile /tmp/tmpThreadId41804289383846930886/haskell/kernel.json
cp /var/cache/pacman/pkg/ihaskell-git2711/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js /tmp/tmpThreadId41804289383846930886/haskell/kernel.js
rm -rf /tmp/tmpThreadId41804289383846930886

Exception:
during copy from: /var/cache/pacman/pkg/ihaskell-git2711/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js to: /tmp/tmpThreadId41804289383846930886/haskell/kernel.js
Exception: /var/cache/pacman/pkg/ihaskell-git2711/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js: openBinaryFile: does not exist (No such file or directory)

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Ping @Jiehong, he maintains the AUR package.

Can you try this with the latest version. I'll try and look into it if the issue persists.

i've updated the Archlinux package with the v<IP_ADDRESS>, and the issue is not there.
@alandao : could you please confirm and close?
Cheers,

Unfortunately I still get the same error message even after updating to ihaskell-git 0.8.2-1 off the AUR. Could be with my environment. I'm new to Juypter so I'm not familiar with what I'm doing, but I already have a Haskell kernel installed to Juypter. Could this be the culprit?
[alan@vbox ~]$ ihaskell install
ihaskell:
Ran commands:
which jupyter
which jupyter
/usr/bin/jupyter --version
which /usr/bin/jupyter
which ihaskell
withTmpDir
rm -f /tmp/tmpThreadId41804289383846930886
mkdir /tmp/tmpThreadId41804289383846930886
mkdir -p /tmp/tmpThreadId41804289383846930886/haskell
writefile /tmp/tmpThreadId41804289383846930886/haskell/kernel.json
cp /var/cache/pacman/pkg/ihaskell-git640/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js /tmp/tmpThreadId41804289383846930886/haskell/kernel.js
rm -rf /tmp/tmpThreadId41804289383846930886
Exception:
during copy from: /var/cache/pacman/pkg/ihaskell-git640/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js to: /tmp/tmpThreadId41804289383846930886/haskell/kernel.js
Exception: /var/cache/pacman/pkg/ihaskell-git640/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux/nightly-2015-08-15/7.10.2/share/x86_64-linux-ghc-7.10.2/ihaskell-<IP_ADDRESS>/html/kernel.js: openBinaryFile: does not exist (No such file or directory)

I also had a haskell kernel when updating (the previous version so).
I haven't managed to reproduce your issue, so I would advise you to try to remove the package altogether, and clean your stack install as well before installing it again, to see if this works (by deleting your ~/.stack for example).
The next build will take some time though…

Closing due to lack of activity. Please re-open if the issue still exists.

The same issue occures when I try to ihaskell install the AUR package :(

@DevWurm It seems that this only happens when using a AUR manager like yaourt.
I'll give it a look, and see what happens with different aur manager such as yaourt and aura.

Well, in Archlinux, I simply am unable to copy the files stack installs locally into the $HOME/.stack directory, simply because this directory is not available when building a package (and for good reasons).
So, as a workaround, under Archlinux the following procedure works:
git clone https://aur.archlinux.org/ihaskell-git.git
cd ihaskell-git
makepkg

As long as you don't delete this directory, of course.
Optionally, perhaps I could make ihaskell static, so that it would work, but would end up bigger.

Or maybe not static, as I'm getting the following issue :/
[2 of 2] Compiling Language.Haskell.GHC.Parser ( generic-src/Language/Haskell/GHC/Parser.hs, .stack-work/dist/x86_64-linux/Cabal-<IP_ADDRESS>/build/Language/Haskell/GHC/Parser.o )
/usr/bin/ld: /usr/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/crtbeginT.o: relocation R_X86_64_32 against `__TMC_END__' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-unknown-linux-gnu/5.3.0/crtbeginT.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status

So, for now, I'm not sure how to solve the primary issue (aka installing with stack with an AUR package). Haskell packages certainly are not that easy to install…

Not working in 2019 either
➜  ~ ihaskell install
ihaskell:
Ran commands:
which jupyter
which jupyter
withTmpDir
rm -f /tmp/tmpThreadId44261-0
mkdir /tmp/tmpThreadId44261-0
mkdir -p /tmp/tmpThreadId44261-0/haskell
writefile /tmp/tmpThreadId44261-0/haskell/kernel.json
cp /home/davo/.cache/yay/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux-tinfo6/fd9772f5a50e4a1edb7b68164a32e7c61f9fa548ec92c7b2fe7ece4f589ac26e/8.6.5/share/x86_64-linux-ghc-8.6.5/ihaskell-<IP_ADDRESS>/html/kernel.js /tmp/tmpThreadId44261-0/haskell/kernel.js
rm -rf /tmp/tmpThreadId44261-0

Exception:
during copy from: /home/davo/.cache/yay/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux-tinfo6/fd9772f5a50e4a1edb7b68164a32e7c61f9fa548ec92c7b2fe7ece4f589ac26e/8.6.5/share/x86_64-linux-ghc-8.6.5/ihaskell-<IP_ADDRESS>/html/kernel.js to: /tmp/tmpThreadId44261-0/haskell/kernel.js
Exception: /home/davo/.cache/yay/ihaskell-git/src/IHaskell/.stack-work/install/x86_64-linux-tinfo6/fd9772f5a50e4a1edb7b68164a32e7c61f9fa548ec92c7b2fe7ece4f589ac26e/8.6.5/share/x86_64-linux-ghc-8.6.5/ihaskell-<IP_ADDRESS>/html/kernel.js: openBinaryFile: does not exist (No such file or directory)

@daviddavo if you're seeing this issue with the Arch package, I don't have any control over that. Please try following the instructions in the README with a fresh clone of the repository and open a new issue if you're still having problems.


How to update and keep history and settings?

Is your feature request related to a problem? Please describe.
There is no description how to update and keep settings and history.
If I just download a new version and execute it, then all the history is lost, also settings are lost.
I would like to keep settings and history.
There is a related issue #61
but if I copy user.config then I get only settings.
I have no idea where the history is stored and how to transfer it into the new version.
Describe the solution you'd like

Please integrate the update check for new versions into the app
Please ensure that settings and history are transfered into a new version
document, how to install a new version in a way which keeps settings and history, if it is not intuitive
document, where settings and history are stored

Describe alternatives you've considered
I did not find a way to get the history into the new version

Hi @aisbergde, your saved network history files are the .sqlite files found under the "C:\Users\User\AppData\Local\OpenNetMeter" folder. You dont have to transfer the history data after updating.
the file structure should look like this,

Regarding the settings files, I'll try to find a solution for it.


Add multi-architecture support for kernel config checker plugin

This adds multi-architecture support to the Kernel Config Analyzer (KCA) plugin.
The Kernel Config Analyzer (KCA) plugin in the Intel Static Analyzer Framework (ISAFW) executes x86-specific checkers regardless of the architecture the analyzed kernel config is destined for. This change enables support for architectures other than x86, such as ARM.
Related discussion:

https://lists.linuxfoundation.org/pipermail/automotive-discussions/2016-August/002438.html
https://lists.linuxfoundation.org/pipermail/automotive-discussions/2016-May/001981.html
https://jira.automotivelinux.org/browse/SPEC-118

Can one of the admins verify this patch?

Oh, this is great, thank you! Was on my mind also, but never got to do this.

test this please

Could you please rebase on top of master? Our CI isn't able to digest non-rebased patches :(

So, yes, after talking to our CI people, I would need this to be submitted to master in order to test in CI. If you do need it jethro also, I can update jethro branch after merging this to master, but it needs to go to master first. Could you please resubmit to master?

Will submit this for master as well.

seems like checksec.sh sha256 and md5sum are broken on master. Should I submit a fix for that first?
WARNING: Checksum failure encountered with download of http://www.trapkit.de/tools/checksec.sh - will attempt other sources if available
WARNING: Renaming /mnt/lbs5/secureplatform_artefacts/rdk_ph1/downloads/checksec.sh to /mnt/lbs5/secureplatform_artefacts/rdk_ph1/downloads/checksec.sh_bad-checksum_57cc3fbbbe48e8ebd4672c569954374d
ERROR: Fetcher failure for URL: 'http://www.trapkit.de/tools/checksec.sh'. Checksum mismatch!
File: '/mnt/lbs5/secureplatform_artefacts/rdk_ph1/downloads/checksec.sh' has sha256 checksum 05822cd8668589038d20650faa0e56f740911d8ad06f7005b3d12a5c76591b90 when 77b8a7fd9393d10def665658a41176ee745d5c7969a4a0f43cefcc8a4cd90947 was expected
If this change is expected (e.g. you have upgraded to a new version without updating the checksums) then you can use these lines within the recipe:
SRC_URI[md5sum] = "57cc3fbbbe48e8ebd4672c569954374d"
SRC_URI[sha256sum] = "05822cd8668589038d20650faa0e56f740911d8ad06f7005b3d12a5c76591b90"
Otherwise you should retry the download and/or check with upstream to determine if the file has become corrupted or otherwise unexpectedly modified.

@hammadahmedirdeto did you clean up your downloads when moving to master (-c cleanall)

yes. simply doing an md5sum and sha256sum on the checksec.sh results in:
~/checksec$ curl http://www.trapkit.de/tools/checksec.sh > checksec.sh
% Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
Dload  Upload   Total   Spent    Left  Speed
100 27977  100 27977    0     0  56627      0 --:--:-- --:--:-- --:--:-- 56748
~/checksec$ md5sum checksec.sh
57cc3fbbbe48e8ebd4672c569954374d  checksec.sh
~/checksec$ sha256sum checksec.sh
05822cd8668589038d20650faa0e56f740911d8ad06f7005b3d12a5c76591b90  checksec.sh
The checksec recipe has the following:
SRC_URI[md5sum] = "075996be339ab16ad7b94d6de3ee07bd"
SRC_URI[sha256sum] = "77b8a7fd9393d10def665658a41176ee745d5c7969a4a0f43cefcc8a4cd90947"
Maybe I am missing something here?

@hammadahmedirdeto the git tree is correct:
$ curl -s http://www.trapkit.de/tools/checksec.sh|tr -d '\r'|sha256sum
77b8a7fd9393d10def665658a41176ee745d5c7969a4a0f43cefcc8a4cd90947  -

(the original .sh seems to have windows style carriage returns and the bitbake fetcher removes those)

oh, yes, checksec issue was reported to me one week ago, but I forgot to submit the fix while travelling, sorry. They changed the way the script is presented and this broke hash. see:
https://github.com/01org/meta-security-isafw/issues/69

I wonder why this works for me and CI for example. Well, I believe #69.

@mythi, I bet CI gets the script from sstate cache, same for you, you do not actually manually fetch the script. I will test the whole thing tomorrow and make a fix

test this please

The reports are produced correctly and CI error is unrelated, merging.


Add BVTs for complianceConfig

This commit tests the ability of complianceConfig to configure compliance in specific situations.
Ref: https://issues.redhat.com/browse/ACM-11661

/unhold

/cherry-pick release-2.11

@JeffeyL you'll have to rebase after #846 is merged since I believe test-e2e-grc-framework will fail.

@mprahl @JeffeyL What's the status here?

@JeffeyL could you please rebase?

Apologies, not sure how I missed this.

/retest

/test ci/prow/test-e2e-grc-framework

/test test-e2e-grc-framework

/retest

@mprahl What's the best way to figure out why test-e2e-grc-framework is failing? I tried looking at the logs but I couldn't deduce much.

@JeffeyL this is unrelated to your PR, so I'll just go ahead and merge it. Let's keep a close eye on this test during the periodic test runs.

/override ci/prow/test-e2e-grc-framework

/cherry-pick release-2.11


[SMALLFIX] close ioer to avoid Java warning

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins/job/Tachyon-Pull-Request-Builder/5809/
Test PASSed.

Out of curiosity, what tooling do you use to check for the resource leaks / Java 6 incompatibility?

LGTM +1

Eclipse shows the Java 6 incompatibilities as errors, and the resource leaks as warnings


VLAN Pool and ranges support

Proposed Functionality
In the VLAN ID Field, allow to select whether it's a single VLAN or a VLAN Pool.  Using a parent-child relationship, we could have a single VLAN Pool with one or more VLANs or VLAN Ranges.

Logic change:  Single or Pool
If Single -> Enter ID
If Pool -> Enter Pool Name -> Add ranges

Use Case
In Cisco's SDN solution, ACI, and I guess in other SDN solutions as well, it's possible to create VLAN Pools, which contain either static or dynamic VLAN allocations using VLAN ranges.  Being able to document this would be really helpful in order to properly plan the VLAN allocations, specially in multi-tenant environments.

Database Changes
Add Pool Name Column
Add Ranges Column
Create relationship between Pool Names and Ranges

External Dependencies
None

The NetBox data model requires each VLAN to be modeled independently. We are unable to deviate from this model for many reasons.


[Screen Readers-Intelligent Support Experience-Start Over]: Voiceover focus is not moving to the multiple buttons that displayed after typing Start Over in the chat box while navigating using right swipe.

Note:
Same issue repros through out the iris chatbot where similar type of control is present.
PWD Impact:
Users who rely on keyboard and screen readers are impacted as Voiceover focus is not moving to the multiple buttons displayed after typing Start Over in the chat box while navigating using right swipe.
Test Environment:
Device: iphone X
OS: iOS version 13.6.1
Microsoft Teams: 1416/1.0.02020061103
Application: Iris-webbot-ppe
Pre-requisite:
Make sure that "Iris-webbot-ppe" app is added to the teams using 'Upload a custom app'.
Repro Steps:
Step 1: Enable Voiceover and Open the teams application and login with valid credentials.
Step 2: Navigate to "Iris-webbot-ppe" chat bot.
Step 3: Type 'Start over' -> Bot response
Step 4: Navigate to buttons present using right swipe and verify whether voiceover focus is moving to the buttons or not.
Actual Result:
Voiceover focus is not moving to the below mentioned buttons that displayed after typing Start Over in the chat box while navigating using right swipe.
1.Customer Invoice Request Button
2.Invoice Adjustment and Correction Button
3.Credit and Rebill Request Button
4.Request SAP Access Button
5.Dispatch Invoice Button
Expected Result:
Voiceover focus should move to above mentioned buttons that displayed after typing Start Over in the chat box while navigating using right swipe.
**Other instance where the same issue repros:
1.Navigation:Start Over->Credit and rebill request->Cancel and rebill request
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Rebilled_focus is not moving_iOS+Voiceover_Other instance 1.png>
2.Navigation:Start Over->Subcon Account Request.
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Subcon Account Request_focus is not moving_iOS+Voiceover_Other instance 2.png>
3.Navigation:Start Over->Subcon Account Request->Yes->99000794
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Subcon Account Request 99000794_focus is not moving_iOS+Voiceover_Other instance 3.png>>
4.Navigation:Start Over->Supplier PO Update
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Supplier PO Update_focus is not moving_iOS+Voiceover_Other instance 4.png>
5.Navigation:Start Over->Customer Success Unit
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Customer Success Unit_focus is not moving_iOS+Voiceover_Other instance 5.png>
6.Navigation:Start Over->Browse by categoary
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_Browse by categoary_focus is not moving_iOS+Voiceover_Other instance 6.png>
7.Navigation:Start Over->How r u?
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_How r u_focus is not moving_iOS+Voiceover_Other instance 7.png>
8.Navigation:Start Over->How r u?->No
please refer the attachment:<MAS 1.3.2_Intelligent Support Service_How r u _No_focus is not moving_iOS+Voiceover_Other instance 8.png>
MAS Reference:
MAS 1.3.2 - Meaningful Sequence

WCAG Reference:
https://www.w3.org/WAI/WCAG21/Understanding/meaningful-sequence.html

By Mistaken copied the bug.


Fix depthai-sdk broken url link

The url for the depthai-sdk is broken (because it has been modified), as a result the homepage link in pypi (https://pypi.org/project/depthai-sdk/) is also broken.
This pull just updates the link in the setup.py for the depthai_sdk.

Thank you!

@ibaiGorordo I just released the 1.1.8 version with these links fixed, thanks again!


Admin Page

While adding faculty position, remove displaying adviser, program and Sr.No fields.

This will need client-side JS to monitor whether the user_type selected is a student or faculty and to hide the adviser/program/sr_no fields when faculty is chosen. This is potentially brittle code that could break if a future version of django changes the field names in the form.
I don't see any simple way of doing this.

I ve also created an admin page

I dont think we need to build a custom admin interface. It seems like a lot of work for more or less replicating the django admin interface.

I ve created a basic user add page. In the django admin page, can we make some fields optional and some fields mandatory? (For ex, advisor id/SRNo is mandatory for students). Do we have to drop page?

We can make fields optional / mandatory. But I don't any easy way of dynamically changing this based on the user_type chosen in the dropdown.

Hey
I am unable to run the server on my local machine as it is giving me this error. I am using the code which I pulled from here. I feel there is an error in the admin page. Could you please have a look into it?
File "/home/vinay/courseRegrWebSite/bheemboy/bheemboy/coursereg/admin.py", line 7, in
from dateutil.relativedelta import relativedelta
ImportError: No module named dateutil.relativedelta
Also which version is running on the server at <IP_ADDRESS>?

This is a cosmetic feature. We will reconsider this issue when we implement the lightweight admin page.


Head not working correctly on catch boundaries

When catch boundaries are hit, styles and other links are not loaded correctly into the head tag.
Error boundaries, however, work completely fine.

Good Catch (pun intended)! Will have a look into this in the coming days.

Digged a little bit into this, here's what I found:

when we just follow the remix guidelines for setting up a catch boundary it wont render styles even when we don't use remix-island.
In order to have styles in a catch boundary, we need to explicitly add <Links /> in there or manually <link /> to them.
In a remix-island app, this would mean we'd want to render <Head /> in the catch boundary
Unfortunately this does not work, either
If we also add <Scripts /> back in our catch boundary we get the styles in the client, but they're missing in the initial server render

From what I understand, remix deliberately does not teat the catch-boundary as part of the route. It's a "hey nothing you configured matches this, we don't know what to do here" scenario. Where it might be just false to add the same links, meta-tags to the page as  the status: 200 version of the same page has.
I'm not sure how to handle this case in remix-island, the first thought coming to mind is that we'd need a CatchBoundaryHead component but that also feels a little strange.
All that said... as written in the pitfalls/notes section of the readme I think it makes sense to move everything global out of remix LinksFunction and MetaFunction and into the static html template in entry.server.ts. And if you put your styles in there you should at least have those loaded on 404 pages.
(I understand that does not help with setting a custom title or tracking for those pages)


Customs serializers

Would be great to have custom serializers in set/get results, or at least JSON, like it is implemented in the main project TaskIQ.

Look, I've checked the code and you can do so. You can set custom serializers in the constructor.

@s3rius , in the backend part it is hardcoded, e.g in "set_result":
        redis_set_params: Dict[str, Union[str, bytes, int]] = {
            "name": task_id,
            "value": **pickle.dumps(result)**,
        }

I see now. Accidentally skipped it. We will add a new parameter to the constructor.


Image expectations problem

Attempting to update my CTS to include #1616 leads to some bizarre image expectations.
Here is one of the failures I'm seeing in images/kernel_read_write for CL_FLOAT images:
[CL_RG   CL_FLOAT                 2] - CL_FILTER_LINEAR - CL_ADDRESS_CLAMP - NORMALIZED
FAILED norm_offsets: -0:
Sample 0: coord {-0.007285(-0x1.dd72a6p-8)} did not validate!
	Expected (0,0,0,1.0625),
	got      (0,0,0,1), error of 0
img size 652 (pitch 5216)
Step by step:
	Filter denormalizes x to -4.750000, 0.000000, 0.000000 (<-0.007285, 0.000000, 0.000000> * <652.000000, 1.000000, 1.000000>)
	Actual integer coords used (i = floor(x-.5)): i0:{ -1, 0 } and i1:{ -1, 0 }
	Array coordinate is 0.000000
	Sampled pixels (rgba order):
		p00: 0.000000, 0.000000, 0.000000, 1.000000
		p01: 0.000000, 0.000000, 0.000000, 1.000000
		p10: 0.000000, 0.000000, 0.000000, 1.000000
		p11: 0.000000, 0.000000, 0.000000, 1.000000
	frac( x - 0.5f ) = 0.750000,  frac( y - 0.5f ) = 0.500000
	ulps: 0.00, 0.00, 0.00, -524288.00  (max allowed: 65538.00)

FAILED: [CL_RG   CL_FLOAT                 2] - CL_FILTER_LINEAR - CL_ADDRESS_CLAMP - NORMALIZED

The A channel for the expectation seems wrong. Am I misinterpreting this message?

<IP_ADDRESS>. Mapping image channels to color values returned by read_image and color values passed to write_image to image channels says that when reading from a CL_RG format, the result value is: (r, g, 0.0, 1.0)

...How did that happen??
Can you give me a log with all the failures?

Here's the rest of the failures for that particular invocation (1D CL_FLOAT kernel_read_write).
test.log

There were also failures with other image types/format. And failures in clFillImage tests too.

What platform? What compile flags?
The failures are primarily in the linear case, which means that something is going wrong averaging the pixels.

What platform? What compile flags?

Also, exactly what make and model of CPU are you running this on? I sure hope it's not an erratum...

What platform? What compile flags?

Also, exactly what make and model of CPU are you running this on? I sure hope it's not an erratum...

@alan-baker Please respond soon. I'd like to fix this sooner rather than later, since it's apparently broken the tests.

I don't have the exact cpu model, but it should be a skylake architecture. Fails in both -O1 and -O3 builds. Platform is Linux. No other compiler flags of note.

So there were a few broken shuffles and an add to a wrong vector that gave the broken results you saw. These should be fixed in #1642. Are there any other broken results that might have been caused by my change? I can't find any.

Hi.
I notice some compilation errors on Intel Compiler which we use for compilation on Windows. Fix is introduced here #1652.
After fixing compilation issues I noticed errors in my results of images tests on Windows (Intel Compiler) and Linux (GNU compiler). The tests were run on Coffee Lake (gen9 platform) and on Tiger Lake (gen11)
Linux errors:
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
test_image_streams CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams max_images CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams test_mipmaps CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams use_pitches CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams read 1D small_images NORMALIZED CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams read 2D small_images use_pitches  NORMALIZED CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_image_streams read 3D small_images NORMALIZED CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
Windows errors:
Intel C++ Compiler 2<IP_ADDRESS>21119
test_image_streams use_pitches CL_FILTER_NEAREST CL_DEVICE_TYPE_GPU
test_cl_fill_images CL_DEVICE_TYPE_GPU
test_cl_fill_images max_images CL_DEVICE_TYPE_GPU
test_cl_fill_images use_pitches CL_DEVICE_TYPE_GPU

@gwawiork do you have all of the other fixes from #1642?  I'm trying to figure out if these are known failures or new failures. Thanks!

@gwawiork do you have all of the other fixes from #1642? I'm trying to figure out if these are known failures or new failures. Thanks!

Yes I've rebuild binaries with these fixes.


Spec: show time in human friendly way in --profile

Before:
$ crystal spec spec/std/int_spec.cr --profile
...

Int compares signed vs. unsigned integers : 0.000459 sec
Int ** raises with negative exponent : 4.3e-05 sec
Int to_s in base raises on base 1 : 1.2e-05 sec
Int ** with float assert : 1.1e-05 sec
Int to_s does to_s for various int sizes with IO : 1.1e-05 sec
Int to_s does to_s for various int sizes : 1.0e-05 sec
Int #chr : 1.0e-05 sec
Int ** with positive Int32 : 9.0e-06 sec
Int to_s in base raises on base 37 with io : 7.0e-06 sec
Int to_s in base raises on base 1 with io : 7.0e-06 sec
Int raises when divides by zero : 7.0e-06 sec

Finished in 1.92 milliseconds
141 examples, 0 failures, 0 errors, 0 pending

After:
$ bin/crystal spec spec/std/int_spec.cr --profile
...

Int ** raises with negative exponent : 34 microseconds
Int compares signed vs. unsigned integers : 33 microseconds
Int to_s in base raises on base 1 : 11 microseconds
Int to_s does to_s for various int sizes with IO : 10 microseconds
Int to_s does to_s for various int sizes : 9 microseconds
Int ** with positive Int32 : 9 microseconds
Int to_s in base raises on base 37 with io : 8 microseconds
Int ** with float assert : 8 microseconds
Int to_s in base raises on base 62 with upcase with io : 7 microseconds
Int to_s in base raises on base 1 with io : 7 microseconds
Int #chr : 7 microseconds

Finished in 1.4 milliseconds
141 examples, 0 failures, 0 errors, 0 pending

Mmh, I'm actually not too sure this is the easiest to read, vs determining the maximum, the unit to represent it as integer and representing all others as fractions of that unit.

I don't know if it matters much, the comparison between spec times, only how long they take. For example:
$ bin/crystal spec spec/std/crypto/* --profile
Using compiled compiler at .build/crystal
.............

Crypto::Bcrypt computes digest vectors : 2.69 seconds
Crypto::Blowfish encrypt and decrypt pair : 32.27 milliseconds
...

Reading "seconds" vs "milliseconds" is already clear there's a huge difference. Showing the second as 0.03227 seconds could work, though it would be a lot more noisy in my opinion.

@jhass after some though, I think normalizing the unit is probably a good idea. This is RSpec's output for --profile:
Top 10 slowest examples (0.03766 seconds, 38.7% of total time):
  Rgviz::Parser parses options
    0.02435 seconds ./spec/rgviz/parser_spec.rb:330
  Rgviz::Lexer lexes or upcase
    0.0039 seconds ./spec/rgviz/lexer_spec.rb:13
  Rgviz::Lexer lexes and
    0.00246 seconds ./spec/rgviz/lexer_spec.rb:7
  Rgviz::MemoryExecutor processes group by with scalar
    0.00176 seconds ./spec/rgviz/memory_executor_spec.rb:293
  Rgviz::Parser parses empty
    0.00132 seconds ./spec/rgviz/parser_spec.rb:47
  Rgviz::Lexer lexes error !
    0.00114 seconds ./spec/rgviz/lexer_spec.rb:73
  Rgviz::MemoryExecutor processes select date "2010-01-02"
    0.00075 seconds ./spec/rgviz/memory_executor_spec.rb:23
  Rgviz::MemoryExecutor processes pivot
    0.00072 seconds ./spec/rgviz/memory_executor_spec.rb:394
  Rgviz::MemoryExecutor processes pivot2
    0.00064 seconds ./spec/rgviz/memory_executor_spec.rb:432
  Rgviz::CsvRenderer renders two rows
    0.00062 seconds ./spec/rgviz/csv_renderer_spec.rb:6

Top 4 slowest example groups:
  Rgviz::CsvRenderer
    0.00078 seconds average (0.00078 seconds / 1 example) ./spec/rgviz/csv_renderer_spec.rb:5
  Rgviz::Parser
    0.00039 seconds average (0.04724 seconds / 122 examples) ./spec/rgviz/parser_spec.rb:5
  Rgviz::MemoryExecutor
    0.00032 seconds average (0.0239 seconds / 74 examples) ./spec/rgviz/memory_executor_spec.rb:5
  Rgviz::Lexer
    0.00018 seconds average (0.02503 seconds / 140 examples) ./spec/rgviz/lexer_spec.rb:5

I like it that the seconds are all more or less aligned, and that you can quickly see where the spec is defined. The "slowest example groups" is nice too, but we can leave that for later.

I thought I commented this before... seems not.
With the last change, the output now looks like this:
$ bin/crystal spec spec/std/int_spec.cr --profile
...

Top 10 slowest examples (0.00021 seconds, 13.98% of total time):
  Int compares signed vs. unsigned integers
    4.0e-05 seconds ./spec/std/int_spec.cr:417
  Int ** raises with negative exponent
    3.4e-05 seconds ./spec/std/int_spec.cr:30
  Int raises when divides by zero
    3.3e-05 seconds ./spec/std/int_spec.cr:325
  Int raises when mods by zero
    2.6e-05 seconds ./spec/std/int_spec.cr:330
  Int #popcount assert
    2.1e-05 seconds ./spec/std/int_spec.cr:404
  Int to_s does to_s for various int sizes with IO
    1.1e-05 seconds ./spec/std/int_spec.cr:267
  Int to_s in base raises on base 1
    1.0e-05 seconds ./spec/std/int_spec.cr:131
  Int to_s does to_s for various int sizes
    9.0e-06 seconds ./spec/std/int_spec.cr:244
  Int #chr
    9.0e-06 seconds ./spec/std/int_spec.cr:441
  Int ** with positive Int32
    9.0e-06 seconds ./spec/std/int_spec.cr:14
  Int gets times iterator
    7.0e-06 seconds ./spec/std/int_spec.cr:335

Finished in 1.5 milliseconds
141 examples, 0 failures, 0 errors, 0 pending

I think that's good enough, even with those "e-05", which can be read as "too fast, don't pay attention to this".


App sidebar mode and optimizations

Change log

Significantly optimizes the performance of the sidebar by lazily computing statistics only for currently visible fields
Added new sidebar modes all|fast|best with updated default behavior that further optimizes the performance of the App for large datasets
Added support for configuring the sidebar mode dynamically in the App and programmatically on a per-dataset basis
Added support for programmatically configuring sidebar groups and default expansion states on a
per-dataset basis

Issues resolved

Resolves https://github.com/voxel51/fiftyone/issues/1607
Resolves https://github.com/voxel51/fiftyone/issues/1914
Resolves https://github.com/voxel51/fiftyone/issues/1270

TODO

[ ] video label tag counts in the grid
[ ] video label tagging

Stale

@benjaminpkane can you add a loading state to the Loading indicators in the filter widgets? Something as simple as animating the dots:
Loading.
Loading..
Loading...

This would help convey that something is happening, like the spinners for the counts.

@benjaminpkane can you add a loading state to the Loading indicators in the filter widgets?
Something as simple as animating the dots:
Loading.
Loading..
Loading...

This would help convey that something is happening, like the spinners for the counts.

Ok, I added the above


Distinct output file for merged PE reads

Hi,
thanks for recently adding the merging feature of PE reads #139 !
Would it be possible to implement a 3rd output parameter in order to separate the merged/unmerged reads in an intuitive way like assemblers (e.g. SPAdes) ask for them?
So, we could immediately end up with cleaned R1, R2 and merged read files.
For example:
fastp -i R1.fastq.gz -I R2.fastq.gz -o R1.clean.fastq.gz -O R2.clean.fastq.gz --out_merged R12.clean.fastq.gz

Maybe worth of a distinct issue but somehow related to this:
What happens with either R1 or R2 reads resulting from successful filtering procedures but lacking a related mate? Could these also be written to a distinct file, like SE reads? Trimmomatic is able to behave that way and thus, those valid reads can be fed into downstream analyses.

What happens with either R1 or R2 reads resulting from successful filtering procedures but lacking a related mate?
If we output R1.clean.fq and R2.clean.fq separately, the unmatched reads should be discard to keep the read name consistent.

Maybe my question was not precise enough. Currently, after passing all quality filters, only valid R1/R2 pairs are written to separate R1.clean.fq and R2.clean.fq files in an ordered manner with consistent read names.
But if for instance R1 passes the quality filters, but R2 of this read pair does not... fastp currently discards the R1 as well. Couldn't you output the passing mate (R1 in this case) to a distinct file only containing unpaired reads? Thus, more high-quality reads can be used in subsequent assemblies, for instance.
Of course, the passing unpaired reads are not ordered anymore, but this would be completely acceptable anyways.
What are your thoughts regarding my the question?

Hi,
a follow up...hopefully this clarifies what I am trying to ask/suggest. Below you find an extract from the SPAdes manual of how to provide PE data:
Paired-end libraries
--pe<#>-1 <file_name>
    File with left reads for paired-end library number <#> (<#> = 1,2,..,9).

--pe<#>-2 <file_name>
    File with right reads for paired-end library number <#> (<#> = 1,2,..,9).

--pe<#>-m <file_name>
    File with merged reads from paired-end library number <#> (<#> = 1,2,..,9)
    If the properties of the library permit, paired reads can be merged using special software.     Non-empty files with (remaining) unmerged left/right reads (separate or interlaced) must be provided for the same library for SPAdes to correctly detect the original read length.

--pe<#>-s <file_name>
    File with unpaired reads from paired-end library number <#> (<#> = 1,2,..,9)
    For example, paired reads can become unpaired during the error correction procedure.

Currently, fastp can serve the R1 (pe-1) and R2 (pe-2) reads after filtering and recently, also merged R12 (pe-m).
In order to utilize as much genome information as possible, it would be great if fastp could:

apply the various quality filters and correction
try to merge R1 and R2
write merged R12 (pe-m) reads to one file, e.g. m.fastq
write unmerged paired reads to R1 (pe-1) and R2 (pe-2) files, e.g. R1.fastq, R2.fastq
write unmerged unpaired reads (pe-s) to another file, e.g. s.fastq

If I got it right, in step 5 R2 reads would have to be reverse complimented before writing them to s.fastq along with residual R1 reads.
Unforutnately, I dont have much knowledge about fastp internals, but by this procedure, fastp could provide merged, paired and unpaired reads in a single step. This would definetly be very beneficial for assembies.
What do you think?
Thanks a lot for considering and best regards!

Hi,
Thanks for your suggestion. I completely understand what you want. But it will make fastp too complicated to implement all of this, and people hate to use complicated tools.
I may first consider to add options to output unpaired R1 and R2.

Hi,
sry for bothering ;-) that's a solid point and I totally agree with you that tools should not be too complicated!
But i guess there isn't so much of additional complexity involved here...
Fastp knows when it deals with PE data due to the -i <input-1-file> / -I <input-2-file> parameters

If the user wants the paired unmerged files, this could simply be implicitly specified by -o <output-1-file> / -O <output-2-file>
If merged reads are wanted, this is currently specified by -m. All you need to add is a related argument, so it would become -m <merged-output-file>
If residual unpaired and unmerged reads are desired, just go for -s <residual-output-file>

So everything that needs to be changed would be a new argument to the -m parameter...
...and in addition, a new optional (and distinct from the merged read functionality) parameter/argument -s <residual-output-file> could be added.
I see that at least the second one can't be implemented right away and might take a while. But I would love to see this on the agenda because, by fulfilling these requirements, fastp would make a giant leap in terms your an ultra-fast all-in-one FASTQ preprocessor credo. Otherwise one had to use several tools or restart fastp with different parameters which is clearly not the way to go...
Best regards!

Just to jump in.
The issue with the unmated reads being included in the clean fastq is one I just bumped into and I definitely agree with you.
So i'm thinking that the unmated reads should go in a separate junk file, essentially R1 no pass.fastq and R2 no pass.fastq. That can include the reads that don't pass other filters as well i think.
Should resolve a lot of pain (at least for me).
Also, very nice tool, especially because its clean and simple to use, which is key.

Just a quick update:
I am implementing the new features, and the new fastp will support 7 separate output files:
1 merged.fq
2 unmerged.R1.fq
3 unmerged.R2.fq
4 unpaired.R1.fq
5 unpaired.R2.fq
6 failed.R1.fq
7 failed.R2.fq
And a --include_unmerged option will be provided to redirect 2~5 to 1.
4 and 5 can be the same file, as well as 6 and 7.

Awesome! thank you so much, this will definitely be super useful

Hi guys, this feature is implemented in fastp v0.19.9 (will be released soon), see the update here:
merge paired-end reads
For paired-end (PE) input, fastp supports stiching them by specifying the -m/--merge option. In this merging mode:

--merged_out shouuld be given to specify the file to store merged reads, otherwise you should enable --stdout to stream the merged reads to STDOUT. The merged reads are also filtered.
--out1 and --out2 will be the reads that cannot be merged successfully, but both pass all the filters.
--unpaired1 will be the reads that cannot be merged, read1 passes filters but read2 doesn't.
--unpaired2 will be the reads that cannot be merged, read2 passes filters but read1 doesn't.
--include_unmerged can be enabled to make reads of --out1, --out2, --unpaired1 and --unpaired2 redirected to --merged_out. So you will get a single output file. This option is disabled by default.

--failed_out can still be given to store the reads (either merged or unmerged) failed to passing filters.
In the output file, a tag like merged_xxx_yyywill be added to each read name to indicate that how many base pairs are from read1 and from read2, respectively. For example,  @NB551106:9:H5Y5GBGX2:1:22306:18653:13119 1:N:0:GATCAG merged_150_15
means that 150bp are from read1, and 15bp are from read2. fastp prefers the bases in read1 since they usually have higher quality than read2.
This function is also based on overlapping detection, which has adjustable parameters overlap_len_require (default 30) and overlap_diff_limit (default 5).

Thank you so much! Also for the super fast implementation, Awesome job!
The new features and command line UI open new possibilities...

Hi, just found a small typo in the usage:
      --unpaired2                      for PE input, if read2 passed QC but read1 not, it will be written to unpaired2. If --unpaired2 is same as --umpaired1 (default mode), both unpaired reads will be written to this same file. (string [=])

-> ...same as --umpaired1 (default mode)...

I just saw that this is still open. I'll create a pull request with a typo fix and close this one.
Again, thanks a lot for this!


Upgrade our issue templates to use GitHub issue forms ✍

Introduction
GitHub has recently rolled out a public beta for their issue forms feature. This would allow you to create interactive issue templates and validate them 🤯.
Appwrite currently uses the older issue template format. Your task is to create GitHub issue forms for this repository. Please use Appwrite's issue templates as a reference for this PR.
Tasks summary:

[ ] Fork & clone this repository
[ ] Prepare bug report issue form in .github/ISSUE_TEMPLATE/bug.yaml
[ ] Prepare documentation issue form in .github/ISSUE_TEMPLATE/documentation.yaml
[ ] Prepare feature request issue form in .github/ISSUE_TEMPLATE/feature.yaml
[ ] Push changes to master and test issue forms on your fork
[ ] Submit pull request

If you need any help, reach out to us on our Discord server.
Are you ready to work on this issue? 🤔 Let us know, and we will assign it to you 😊
Happy Appwriting!

Hi @TorstenDittmann Can I work on this issue?

can i work on this issue?

@KKVANONYMOUS  @vendz  Looks like you have some issues assigned to you already. We request you to complete those before requesting assignments on new ones. Also, please consider picking a different type of issue so other contributors can try this one.

@christyjacob4  Can I work on this?

@Sin-Sumit Looks like you have some issues assigned to you already. We request you to complete those before requesting assignments on new ones. Also, please consider picking a different type of issue so other contributors can try this one.

@Meldiron I completed my previous assigned issue and thank you for your help, can I work on this?

@Sin-Sumit Please pick a different type of issue, so others can also try this one 🙏 Here are some cool suggestions:
https://github.com/appwrite/demos-for-functions/issues
https://github.com/appwrite/appwrite/issues/1774
https://github.com/appwrite/appwrite/issues/1775
https://github.com/appwrite/appwrite/issues/1773

Thank You @Meldiron

@KKVANONYMOUS @vendz Looks like you have some issues assigned to you already. We request you to complete those before requesting assignments on new ones. Also, please consider picking a different type of issue so other contributors can try this one.

ohhkk...Thanks @christyjacob4

@TorstenDittmann may I be assigned to this issue? I've already raised a PR for this, and I've not worked on it before 😄

Hi @Meldiron, can this issue be assigned to me?

@Bharat123rox  Please create your PR after you've been assigned to an issue.
@Sangwan5688 All the best :+1:


Dropping support for 2.0.0

I removed 2.0.0 from the Travis build matrix as MRI 2.0.0 is no longer supported.
I plan to drop support for 2.0.0 gradually, since it gives some overhead when writing new specs (more guards) and makes more complicated to test 2.1 syntax like keyword arguments.
I made a tag drop_support_for_2.0.0 to note the last compatible version.
If somebody has a strong objection, I am open to reconsider.

No objection so closing :smiley:


modules/terraform/var-file.go:142:8: undefined: hcl.Decode

Latest release is causing an error:
vendor/github.com/gruntwork-io/terratest/modules/terraform/var-file.go:142:8: undefined: hcl.Decode
FAIL	git.*******.com/mongodbatlas-tf/terratest/mongodbatlas-cluster [build failed]
FAIL

Exited with code exit status 2

https://github.com/gruntwork-io/terratest/blob/88ba3f070a939aca8351eae616a3c899bfe28b91/modules/terraform/var-file.go#L142

@brikis98
@alpacamybags118

Problem started with #733

Apparently this version breaks compatibility with go dep.
Had to switch from
dep init && dep ensure -vendor-only
to
go mod init git.rockfin.com/mongodbtatlas-tf && go mod vendor

I think the root of the issue is dep is trying to pull v2 of hcl while the go mod of the terratest library explicitly referenes v1, so dep isnt respecting the libraries required version

@alpacamybags118, @WafflesMcDuff I got the same error when running go get -u github.com/gruntwork-io/terratest/modules/terraform in our pipeline. I was wondering how can I use the previous releasein the meantime. I will appreciate your piece of advise.

Confirming, having same problem with the recent changes. Testing, trying to find a workaround.

As WafflesMcDuff mentioned, use
go mod init
instead of
dep init

This is indeed a bug as we should be using hclv2. Will work on updating the library function to use hcl v2 asap.

This issue is affecting me as well. Part of the pipeline we wrote ensures we always use the latest terratest version so it has been broken and preventing any tests from actually running.

Potential fix for this was released https://github.com/gruntwork-io/terratest/releases/tag/v0.32.8
Please try it out and see if it resolves this.

Unfortunately I am still having this issue. I assume that is why you re-opened the issue, but wanted to comment in case you were unaware.

Can you share with me the error message you got? It should be different since the call to hcl.Decode is no longer in the source code.
If you are still getting the same error message, then you need to bump terratest in your go.mod.

It is different now. Is this a separate issue or still the same issue?
package command-line-arguments (test)
	imports github.com/gruntwork-io/terratest/modules/terraform
	imports github.com/hashicorp/hcl/v2/hclparse: cannot find package "github.com/hashicorp/hcl/v2/hclparse" in any of:
	/usr/vsts/pipeline-agent1/_work/_tool/go/1.13.5/x64/src/github.com/hashicorp/hcl/v2/hclparse (from $GOROOT)
	/home/Azureuser/go/src/github.com/hashicorp/hcl/v2/hclparse (from $GOPATH)

Ah yes this is a separate issue. Can you try running go mod tidy to see if that resolves your issue?

I was able to fix my new issue with GO111MODULE=on as per https://github.com/hashicorp/hcl/issues/371 so your update to terratest resolved my problems. Thank you.

Thanks for confirming! Will close this issue then. Please open a new issue if you run into other issues with go dependencies!


Kosmos docstrings are not working with builder_method decorated methods

Any builder_method decorated method will show the wrapper_function docstring instead of the original decorated method's.
For example, try
j.builder.runtimes.golang.install?

This will show
wrapper_action(*args, **kwargs)

branch: development_builder commit: 9aec0b76024d16b5e2f3d78b14ab4dc0b9e1f3e9
Verified


feat(command-feature): respond an embed error message when the feature name is empty

PR Checklist
Please check if your PR fulfills the following requirements:

[x] The commit message follows our guidelines
[x] Tests for the changes have been added/updated (for bugfix/feature)
[ ] Docs have been added/updated (for bugfix/feature)

PR Type
What kind of change does this PR introduce?

[x] Feature (a new feature)
[ ] Bugfix (a bug fix)
[ ] Style (changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc))
[ ] Refactor (a code change that neither fixes a bug nor adds a feature)
[ ] Perf (a code change that improves performance)
[x] Test (adding missing tests or correcting existing tests)
[ ] Build (changes that affect the build system, CI configuration or external dependencies)
[ ] Chore (anything else), please describe:

What is the current behavior?

What is the new behavior?
Does this PR introduce a breaking change?

[ ] Yes
[x] No

Other information
Fixes #767.

@all-contributors add @asmodee-bellanie to review.

@vvalembois he's back 😄
Well you miss all the Firebase features (the real pain was there and having a second thought about the conception of the whole thing would have been great).


Error printing to logs from Godot is not rate limited

Godot version:
3.2.3.stable.mono (also previous versions at least as far back as 3.2.1)
OS/device including version:
GLES3, both Windows and Linux
Issue description:
When Godot engine encounters an error, it prints it to logs. It's good that all error text is printed (and ignores normal print limit per second), however I've experienced this a few times and gotten reports from players, that in some cases when Godot really locks up on some error, it will infinitely spam an error message as fast as possible.  I can't guarantee this, but I've also received 3 reports total that my game, that uses Godot, has caused the user's computer to totally lockup, and in 2 cases rebooting and trying to run the game again didn't work (the game files had become corrupted). So I very strongly think that there needs to be some limit in all Godot error printing to stop gigabytes of logs being generated that freeze computers.
This issue is related to: https://github.com/godotengine/godot/issues/37652 however this is not the same, as I'm saying that all of the error printing code should have an inbuilt fail-safe to kill the process before ridiculous amounts of repeating logs are printed.

Game using Godot froze / locked up (presumably) in a physics related bug. Instead of the game properly crashing and process exiting, instead the process just stayed open printing the same repeating error in log files that ended up taking gigabytes of space. I expected that the engine would have some kind of fail-safe to just give up on writing logs at some point.
I tried to find an issue about this, but I only found specific cases where infinite errors are printed, and not a general report about the problem of really big log files.
Steps to reproduce:
Enable logging to a file, then hit a very serious bug in godot, for example https://github.com/godotengine/godot/issues/37652 and wait some time while Godot is frozen to generate really big log files.

If this is about Mono logs, this is a duplicate of https://github.com/godotengine/godot/issues/21895.

If this is about Mono logs, this is a duplicate of https://github.com/godotengine/godot/issues/21895.

If this is about Mono logs (which are separate from engine logs), this is a duplicate of #21895.

That's not a Mono specific issue, though Mono does make the issue more critical as it tends to be quite spammy.

As for the issue mentioned here, I'm not sure if we can do much about it. If we disable writing to a file once the log has exceeded a certain size, we risk losing out on important information especially if the process does end up exiting at some point in time.

At that point I don't think it matters, if your logs are 2 GB most users wouldn't even be able to extract the tail of the log which might possibly contain useful info (and most likely wouldn't).

If this is about Mono logs (which are separate from engine logs), this is a duplicate of #21895.

That's not a Mono specific issue, though Mono does make the issue more critical as it tends to be quite spammy.

As for the issue mentioned here, I'm not sure if we can do much about it. If we disable writing to a file once the log has exceeded a certain size, we risk losing out on important information especially if the process does end up exiting at some point in time.

At that point I don't think it matters, if your logs are 2 GB most users wouldn't even be able to extract the tail of the log which might possibly contain useful info (and most likely wouldn't).

This is not about mono logs. It's these logs that I mean, that are from the game and from Godot engine:

I don't usually look at the mono logs and I haven't instructed any players to look at them either.
So far each time a single message repeats forever. I don't really have a good suggestion on where to draw the line, but detection on when to stop, could rely on detecting that the last message just repeats for megabytes worth of logs.

At that point I don't think it matters, if your logs are 2 GB most users wouldn't even be able to extract the tail of the log which might possibly contain useful info (and most likely wouldn't).

Exactly, some users even asked me advice on what tool to use to even open a log that is so large so that they could post the first few megabytes for me to seen.

This is not about mono logs. It's these logs that I mean, that are from the game and from Godot engine:

I don't usually look at the mono logs and I haven't instructed any players to look at them either.
So far each time a single message repeats forever. I don't really have a good suggestion on where to draw the line, but detection on when to stop, could rely on detecting that the last message just repeats for megabytes worth of logs.

At that point I don't think it matters, if your logs are 2 GB most users wouldn't even be able to extract the tail of the log which might possibly contain useful info (and most likely wouldn't).

Exactly, some users even asked me advice on what tool to use to even open a log that is so large so that they could post the first few megabytes for me to seen.

I'm not sure how to fix this.

Limiting to a given file size (such as 20 MB) isn't a good idea for servers or persistent processes since these can run for months with no interruption.
Limiting using a timer isn't a bad idea, but I don't think we can use Timer nodes or stuff like that in the rotating file logger since it's a core API that should work without a scene tree.
Detecting endless message loops is difficult as you may have more than 1 message being printed in a quick succession (such as a chain of 3-4 messages).

Any ideas?

I'm not sure how to fix this.

Limiting to a given file size (such as 20 MB) isn't a good idea for servers or persistent processes since these can run for months with no interruption.
Limiting using a timer isn't a bad idea, but I don't think we can use Timer nodes or stuff like that in the rotating file logger since it's a core API that should work without a scene tree.
Detecting endless message loops is difficult as you may have more than 1 message being printed in a quick succession (such as a chain of 3-4 messages).

Any ideas?

Fixing this would also be necessary before we can enable saving editor logs to files too, and not just project logs. Just like Mono, the editor can be pretty spammy as it's easy to trigger errors in a process callback while developing.


How can I set the center point to 0, fix the maximum value to 100, and not require my data to include the maximum value?

Radar chart, how can I fix the maximum value to 100, the minimum value to 0 (center point), even if my dataEntries may not include 100. Currently, I noticed that the scale adjusts based on the maximum value in dataEntries, but my values may not always include the maximum value (100). How should I handle this?
                RadarDataSet(                   // 设置数据内部的颜色                   fillColor: ColorStyle.system40_0054a7,                   // 设置数据边框的颜色                   borderColor: ColorStyle.system_0054a7,                   //设置数据边框的宽度                   borderWidth: 2,                   //设置数据点的半径(点的大小)为0来隐藏它们                   entryRadius: 0,                   dataEntries:  [                     RadarEntry(value:0),                     RadarEntry(value: 0),                     RadarEntry(value:0),                     RadarEntry(value: 90),                     RadarEntry(value: 70),                     RadarEntry(value: 50),                   ]                 ),

Versions

flutter sdk: '>=3.0.6 <4.0.0'
fl_chart: ^0.63.0

I want it to display a maximum value of 100 and a minimum value of 0 (displayed at the center point).

code:

Have the same issue here. Thanks for the great work!


How to use Multiple API with single cognito

Which Category is your question related to?
Appsync API,  Cognito
Amplify CLI Version
4.17.1
How to use Multiple API with single cognito(userpool).

Hello @anarerdene
Currently using the same Cognito Userpool in different APIs is not supported. We have an RFC open for this.
RFC: https://github.com/aws-amplify/amplify-cli/issues/3977
Please follow this thread for updates.


Promotion

It is a gross oversight that each developer has to hack up a solution to allow their users to select which piece they want to promote to. There should be some standard way of doing this. See issue #49.

I'm a little confused. Do you have an algebraic from / to square and want to figure out if the move is a promotion prior to making it?
const chess = Chess('7k/4P3/8/8/8/8/8/7K w - - 0 1')

const from = 'e7'
const to = 'e8'

const isPromotion = chess.moves({ verbose: true })
                         .filter((move) => move.from === from &&
                                           move.to === to &&
                                           moves.flags.includes('p')).length > 0

if (isPromotion) {
    const promotion = promptUserForPromotionPiece() // <- you supply this
    chess.move({ to, from, promotion })
} else {
    chess.move({ to, from })
}

Like this?

I feel a little confused here too, and I think the API may be to blame. Prompting-For-Promotion-Piece is not really a fringe requirement. There should be a succinct way to do this. I think the way you just showed should be sufficient. Alternatively, a checkMove() method would make this task more readable.
const chess = Chess('7k/4P3/8/8/8/8/8/7K w - - 0 1')

const from = 'e7'
const to = 'e8'

const validMove = chess.checkMove({ to, from })

if (validMove && validMove.isPromotion){
    const promotion = promptUserForPromotionPiece()
    chess.move({ to, from, promotion })
}

It may be hard to envision the perfect API for this. And if designing a better API that covers this fairly common requirement is too difficult, then at the least, there needs to be better documentation on the issue than the one solution provided on issue #49 that's consists of instantiating a new Chess engine just to check if the move is a promotion move.

#131 related

@jhlywa Any news here? This is an important feature if building an interactive game.

I like the proposed chess.checkMove solution. Otherwise getting the value is simple, and would be different based on how you are building your game.


// Just leaving good vibes and good feedback! Thanks for an excellent coding tool!

Product and Version [VS/VSCode]:
OS Version [macOS/Windows]:
Live Share Extension Version:
Target Platform or Language [e.g. Node.js]:
Steps to Reproduce / Scenario:

Positive feedback! Thanks for such an awesome product!


Nil type check fails when using ensure

require "spec"

describe "not_nil!" do
  a = 0
  a + 1 # > undefined method '+' for Nil (compile-time type is (Int32 | Nil))

  it "can be nil?" do
    a + 1 # > undefined method '+' for Nil (compile-time type is (Int32 | Nil))
    a.not_nil!
    a + 1 # > undefined method '+' for Nil (compile-time type is (Int32 | Nil))
  end
ensure
  a + 1 # > undefined method '+' for Nil (compile-time type is (Int32 | Nil))
end

Compile time type should not include Nil here?
Crystal 0.24.2 (2018-03-10)

LLVM: 5.0.1
Default target: x86_64-apple-macosx

Reduced:
def foo(&block)
  block
end

foo do
  a = 0
  a + 1
ensure
  a + 1
end

More reduced:
begin
  a = 0
ensure
  a + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
end

In general, there could be some error before assigning to a which would leave it as Nil in the ensure block. In this case with assigning a primitive there are probably not many chances (if any?) that this happens.  But I don't think it would be wise to implement a special treatment for this.

No, because with sequential expressions, a + 1 will never be executed if a = 0 raises. But in an ensure block, it will even if a = 0 failed.

Reduced again:
def foo(&block)
  block
end

foo do
  a = 0
  foo do
    a + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
  end
ensure
  a
end

This time the error above makes little sense.

Btw, you can replace the outer foo do with begin.

With proc
begin
  a = 0
  a + 1
  -> do
    a + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
  end.call
ensure
  a.not_nil! + 1 # This makes sense, at least when a is not primitive
end

Adding a statement after the proc makes thing even weirder:
begin
  a = 0
  a + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
  -> do
    a.not_nil! + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
  end.call
  a + 1 # undefined method '+' for Nil (compile-time type is (Int32 | Nil))
ensure
  a.not_nil! + 1 # This makes sense, at least when a is not primitive
end

Is there any update on this?
I'm looking for a workaround https://stackoverflow.com/q/59453429/1260906


SentencePiece and dict.CN_char.txt

Hello, thanks for your great work! I would like to know the SentencePiece's vocabulary size and content are same as dict.CN_char.txt. I need to deal with Chinese-English mixed correct problems and correct some Chinese to English, should I need to train a new SentencePiece model and get a new dict.CN_char.txt?Thank you!

Really thanks for your reply! In fastcorrect, the word can only be split by space? I use the SentencePiece model provided , and there are some subchars as a token thus making the correct results be . For example, '我喜欢苏学课',use the SentencePiece model I got the token '_我 喜欢 苏学 课',and the output is '我课'.But When I use '我 喜 欢 数 学 课',it got right result. In a word, the SentencePiece model is only used to get a CN_char.txt? So the alignment way only supports char2char because all tokens only have a char ？In your dict.CN_char.txt, I think it is one char, Thank you very much！


Update a record not working

Bug report
Describe the bug

Hello, while trying to update a record an Exception of type NullReferenceException.
After debugging the exception is thrown when calling the Update method in Builder class while initializing the QueryFilter object whit a null criteria the Helper method GetPropertyValue doesn't retrieve the value of the primary key property it returns null.
I figured it out instead of using the Helper method I used the PrimaryKeyValue Property of the model and worked perfectly. I submitted a PR :relaxed: for this case if is it ok.

Second thing is when trying to update a non-existing user another exception is thrown of type JsonSerializationException. The issue is the Postgrest returns an empty array "[]" when trying to update a non-existing record and the Helper method MakeRequest when not a success status code is returned tries to deserialize the response content to an ErrorResponse object, an empty array cannot be deserialized to ErrorResponse.

Thank you.
To Reproduce

Retrieve a user

var user= await client.Builder<User>().Filter("username", Postgrest.Constants.Operator.Equals, "supabot").Single();

Update if not null

user.Status = "OFFLINE";
await user.Update<User>();

To reproduce second case (Not Found user)

var user = new User
{
   Username = "ghost",
   Status = "ONLINE"
};
await client.Builder<User>().Update(user);

Expected behavior

User updated if not null
When trying to update a not existing user a RequestException to be thrown instead of JsonSerializationException

System information

OS: [Windows 10 Pro 1909]
.Net core 3.1.x
Visual Studio 16.8
Version of supabase-postgrest-csharp: master branch of current repo

Expected Behavior #2 is fixed in commit f51d8a6c
Thanks again for a detailed bug report!


Enable on-type formatting from language server

For #2690.
Similar to #2612. Note that :-based formatting isn't implemented in language server yet (Microsoft/python-language-server#165), but it hasn't been enabled in the extension for anyone for a while now either (fixed in #2714/#2724).
Since line formatting is relatively new in language server, this likely shouldn't make it out into a release until the language server downloaded by default is new enough to include that functionality. I haven't been monitoring that side of things, so feel free to hold off on merging this until the right time.

[x] Pull request represents a single change (i.e. not fixing disparate/unrelated things in a single PR)
[x] Title summarizes what is changing
[x] Has a news entry file (remember to thank yourself!)
[x] ~Unit tests & system/integration tests are added/updated~
[x] ~Any new/changed dependencies in package.json are pinned (e.g. "1.2.3", not "^1.2.3" for the specified version)~
[x] ~package-lock.json has been regenerated by running npm install (if dependencies have changed)~

Turns out I forgot to add the news file before I made the PR (so it's good that this was waiting and not merged). It's added now.

For reference, a block formatting port was merged in PLS in Microsoft/python-language-server#217.


A few questions about the formulas in the flux differencing tutorial

I would like to know if f* and f*surface  , which are both numerical fluxes in the second formula from the image, have any differences. Additionally, are f_vol（u，u）,f_vol（u+，u-）and f_vol all two-point fluxes? What are their differences? Is it just a matter of notation, or are their specific forms different?

f_vol, f_central, and f_surface will all be two-point fluxes. However, the first two are symmetric central or "central-like" fluxes and are generally non-dissipative.
The surface flux is often chosen to be dissipative; it is also not symmetric in general.

@teddyz1999 Does this answer your questions? If so, could you please close this issues (as completed)?


Add the fuzz testcase from #20821

An infinite loop was identified via a fuzz testcase in openssl/openssl#20821. We add it to the corpora.
See also openssl/openssl#20824

ping for second review @openssl/committers

Pushed. Thanks.


Adding another action point

I recall that this was suggested as action point (be my) and accepted, but please correct me if I am mistaken.
Also fixed a small typo.

Thanks @lexnederbragt for the update. Honestly, after the meeting was over I felt unclear about the decision we landed on about the membership tier. It is absolutely fine by me to write a proposal. And I remember that @ainor-star will take the announcement email list.


i got killed while using dino_vits8

I'm trying to use pre-trained dino_vits8 but got killed when used it with my dataset .. does each one of the pre-trained models like dino_vits8 and dino_vits16 depend on the number of GPU or has its own specifications ?

I think ViT-S/8 requires more memory than ViT-S/16. It could be the reason.

excuse me .. can I take your email to discuss the paper with you if you please ? i have questions in the idea, not in the coding :-)
Appreciate your help

Thanks a lot .. i will do that :-)


test

test

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test2

Pull request in error from a workshop run.


Change TableMapper Contract

select() should return an array of rows (arrays) ie from pg_fetch_all() or null (nothing found)
insert() should return the primary key value if a primary key exists or null (insert worked)
update(?string $returnColumnName) should return the returnColumnName if set, or primary key value if a primary key exists or null (update worked)
delete(?string $returnColumnName) should return the returnColumnName if set, or primary key value if a primary key exists or null (delete worked)
Note that all use QueryBuilder::execute(), which throws an exception if a query fails, so no need to return false in the above method.

There are no delete and update methods. There are deleteByPrimaryKey and updateByPrimaryKey, the contracts for them should be as follows:
updateByPrimaryKey($primaryKeyValue, ?string $returning) should return the returning value if set or the primary key value
deleteByPrimaryKey($primaryKeyValue, ?string $returning) should return the returning value if set or the primary key value
Note that returning does not have to be a column name. It could be a sql expression.

Actually for delete. and possibly update, I'm going to remove returning functionality in order to simplify as it's not being used, and no sense returning the primaryKeyValue as it's the only argument, so the return is void.


Scrolling with touchpad get weird sometimes

Environment
Windows build: 21382.1
Distribution: debian 11
WSLG : 1.0.21
Steps to reproduce
Scroll up and down with touchpad.
Expected behavior
It should scroll to some certain direction
Actual behavior
Sometimes it keeps shaking up and down violently even though you scroll towards only up, or down.
This doesn't happen in 1.0.19 but happens once in a while in 1.0.20. It happens often in 1.0.21

Hello, in which app are you seeing this?

Hello, in which app are you seeing this?

CLion

Hi, same or similar issue on WSLg ( x86_64 ): 1.0.22. Strange but i have problem only scrolling downwards (especially fast scrolling). Scrolling up seems to work fine both with touchpad and mouse.
Scrolling down is shaking, jerky most of the times using the touchpad. Though scrolling very very slowly is ok.
Using a mouse, the situation is much better, but still scrolling pretty fast (eg logitech free spin wheel) it's just shaking.
Tested on HP ProBook 455 G7
WSLg ( x86_64 ): 1.0.22
Win 10 Pro 10.0.21390
Reproduced on in phpStorm and gedit.

Hi, same or similar issue on WSLg ( x86_64 ): 1.0.22. Strange but i have problem only scrolling downwards (especially fast scrolling). Scrolling up seems to work fine both with touchpad and mouse.
Scrolling down is shaking, jerky most of the times using the touchpad. Though scrolling very very slowly is ok.
Using a mouse, the situation is much better, but still scrolling pretty fast (eg logitech free spin wheel) it's just shaking.
Tested on HP ProBook 455 G7
WSLg ( x86_64 ): 1.0.22
Win 10 Pro 10.0.21390
Reproduced on in phpStorm and gedit.

It looks like all members of the Jetbrains' family have this issue ?

Hi, same or similar issue on WSLg ( x86_64 ): 1.0.22. Strange but i have problem only scrolling downwards (especially fast scrolling). Scrolling up seems to work fine both with touchpad and mouse.
Scrolling down is shaking, jerky most of the times using the touchpad. Though scrolling very very slowly is ok.
Using a mouse, the situation is much better, but still scrolling pretty fast (eg logitech free spin wheel) it's just shaking.
Tested on HP ProBook 455 G7
WSLg ( x86_64 ): 1.0.22
Win 10 Pro 10.0.21390
Reproduced on in phpStorm and gedit.

I have the same problem on WSLg 1.0.24.
I also have this issue with google chrome.
Tested on Thinkpad T14 Gen 1 AMD

Same issue with gedit or Intellij.
Tested on Razer Blade 14 2021 with WSLg 1.0.26

Likewise.  I don't encounter any scrolling anomalies when using a mouse but with my laptop's touchpad (Asus G15 2021) it seems conditional. Gesture (2 finger) scrolling up/down slow and quick without lifting my fingers works perfectly fine but the moment I lift my finger and attempt to do fast kinetic scrolling it'll get confused and repeatedly scroll up/down and jitter randomly until the momentum has come to a halt, this does not happen when I do a slow to normal speed kinetic scroll.  It occurs with any WSLg app for me.  CLion, Chromium, ..., gedit.
ayserjamshidi@AYSERS-LAPTOP:~$  cat /mnt/wslg/versions.txt
WSLg ( x86_64 ): 1.0.26+Branch.main.Sha.26ce2c09b86442f3c7f4f6462f770ed2afa76a25
Mariner: VERSION="1.0.20210224"
FreeRDP: b05321cd4e6a862aef76163a69db4e1910245736
weston: 46756d0e77e5c01b5995fbbee6f3ab0db9b30612
pulseaudio: 2f0f0b8c3872780f15e275fc12899f4564f01bd5
mesa:

Stock WSL kernel and the most up-to-date packages (as of Nov 1st, 2021) with no added third party repos.

same issue like in comment above, same versions
"the moment I lift my finger after doing a fast kinetic scroll it'll get confused and repeatedly scroll up/down"
Reproduced in google chrome, webstorm .

Looks like it was fixed in the recent version. I have just updated to the version from Microsoft Store, and the issue seems gone now.
WSL version: <IP_ADDRESS>
Kernel version: <IP_ADDRESS>
WSLg version: 1.0.47
MSRDC version: 1.2.3575
Direct3D version: 1.606.4
DXCore version: 10.0.25131.1002-220531-1700.rs-onecore-base2-hyp
Windows version: 10.0.22621.819

@miszczu, yes, this issue has been fixed in Store version, thanks!


Clean up and clarify documentation

Several people have been confused about the unit of the rate, so make it clear that it's a per-second rate. Also fix various formatting issues to bring this plugin in line with with others. This addresses parts of the confusion in #29.

@logstash-plugins/logstash-core—nine-week review ping for this documentation-only change.

LGTM

@jsvd, if we're not waiting for someone else to weigh in could you please merge the PR? I don't have permissions to do so myself.


Names for high-level Variation categories

Below we consider new names for what to date we have been calling 'Sequence-Level Variation' vs 'Post-Sequence Variation', and for what to date we have been calling 'Precise Variation' vs 'Bucket Variation'.
But before considering names proposed in this ticket, we need to be  absolutely sure that we agree on the meaning of the concepts we are naming. Once we have a common understanding of the concepts, we will be in a better position to agree on the best name to give them.  Toward this end, see the gdoc here where the concepts we want to name are described.
@ahwagner, @larrybabb consider yourselves tagged. All, feel free to edit directly to change/add new proposals.

I.  'Sequence-Level Variation' vs 'Post-Sequence Variation' (original names)
Sequence-Level Variation =  changes in the sequence of a macromolecule that caries genetic information.

inclusive of different molecule types - genomic, transcript or protein
inclusive of  different levels of organization - e.g. an allele representing a single continuous sequence variation; a haplotype representing a collection if linked, in cis alleles; or a genotype representing a collection of in trans alleles at a particular location.

Post-Sequence Variation =  variable states of a genetic program 'downstream' of sequence (typically related to the expression/regulation of a particular gene product) Examples include:

Variation in expression level of a gene (normal, increased, decreased)
Variation in expression location of a gene (normal, shifted to different cellular compartments)
Variation in epigenetic alteration/state of a gene/region (e.g.  normal, increased, decreased methylation)
Variation in relative abundance of different transcripts/protein isoforms of a gene

Naming proposals

Sequence-Level Variation vs Post-Sequence Variation (original names - may want to change?)
Sequence Variation vs Non-Sequence Variation
Sequence-Level Variation vs Other Molecular Variation
Sequence-Level Variation vs Molecular State Variation

II. 'Precise Variation' vs 'Bucket Variation' (original names)
Precise Variation =  a particular instance of variation in sequence, as represented in a  particular syntax/format (e.g. HGVS, VCF, SPDI), grammar (e.g. right-shifted),  and with respect to a particular reference (e.g. GRCh38 NC_000019.10).

one reason we want to move away from calling these "precise" is that it suggests the exact sequence and location is known. But this is not the case - the sequence or location may be imprecisely known/specified. The key here is that these aim to describe a single, specific variation at a particular location in a genome (whether the location is completely known or not)
Precise variants can be defined at the genomic (e.g.  NC_000019.10:g.44908684T>C), transcript (e.g. NM_000041.3(APOE):c.388T>C (p.Cys130Arg), or protein (e.g. NP_000032.1:p.Cys130Arg) level.

Bucket Variation =  a rule-based class or category of variation, defined by top down membership criteria, and inclusive of any precise variant or genetic state that meets these criteria.

These can define classes of 'sequence-level variation', e.g. "any deletion spanning exon 3 of the EGFR gene", "any fusion between the BRAF and CUL1 genes", "any frameshift mutation in the first two exons of the BRCA2 gene",  "any activating mutation in the KRAS gene", "any variation resulting in amplification of the ALK gene"
Or these can define classes of 'post-sequence variation', e.g. "any increase in expression of IGF2", "any hypo-phosphorylation of HER2", "any increase in phosphorylation of eIF2alpha Serine 51", “any reduction in methylation of region X of chromosome 12"

Naming proposals:

Precise Variation vs Bucket Variation (original names, but need to change)
Variation Instance vs Variation Class
Particular Variation vs Rule-Based Variation
Variation Instance vs Variation Rule
Variant vs Variation Selector (LB)

I came across this text in an email thread between Alex and Peter Robinson, that raised an important possible point of confusion that should be clarified:

"One of the things we've been actively working on in GKS is bridging consensus-level variation (we currently describe this as variation classes, though the terminology is subject to change) with observation-level variation (variation instances–the sort of thing VCFs were designed to capture). The VICC is full of variation class knowledge. . . "

This raises a possible issue with the use of 'Instance' vs 'Class' to distinguish the two high-level categories of variation in our model - as an instance vs class dichotomy may be interpreted as the former representing observations of variants in a particular patient (e.g. NC_000019.10:g.44908684T>C in Patient 1), and the latter representing an abstract, knowledge-level variant (e.g. NC_000019.10:g.44908684T>C in general, independent of patient context . .  the kind of variation that KBs like ClinVar annotate with knowledge).
This observation-level vs knowledge/consensus-level distinction is NOT what our instance vs class dichotomy is meant to reflect. ALL variation in our data/models are considered abstract, knowledge/consensus-level concepts that are independent of patient context. Conceptually, this means that multiple patients can share the same variation - i.e. we would not create separate instances for  NC_000019.10:g.44908684T>C in patient 1 vs NC_000019.10:g.44908684T>C in patient 2.
Rather, the 'Instance' vs 'Class' distinction we make is intended to separate particular abstract/knowledge-level variations from or a rule-based sets of particular variations which all share  some specified characteristic(s). So perhaps a better naming convention is to set ‘Particular Variation’ apart form ‘Rule-Based Variation’ (and being sure to clarify in documentation that both of these refer to knowledge/consensus-level variation, as opposed to observation-level variants).

This is a great point. Being the author of the above quoted text, and understanding this concept the same way @mbrush defined it, specifically:

... the 'Instance' vs 'Class' distinction we make is intended to separate particular abstract/knowledge-level variations from or a rule-based sets of particular variations which all share some specified characteristic(s).

In retrospect, my casual conveyance of this concept (regretfully) would naturally be interpreted this way. I agree that the use of Variation Rule or Rule-Based Variation vs. Particular Variation or Specific Variation is a good naming convention to avoid this confusion.

@ahwagner this is helpful.
In the original "variation profile" or "molecular profile" concept you introduced from JAX lab, it seemed as if there were "profile" configurations that permitted the combination of Rule-Based+Particular Variations together.
Request for info 1:
I'd really like to see some real world use cases for this. My guess is that when a profile has multiple 'members' they are either all of one type or the other. (at least I'm hoping that is the case for the sake of simplifying the model and its application.)
Request for info 2:
I recall that you also conveyed that there could be a 'nesting' of profile concepts (more than 1 level). Is it possible this would only be for rule-based profiles? Again, examples to represent the breadth of these nested sceanrios might help bring some clarity into how this can be applied. Again, my guess is that for the rule-based nesting there's some need to 'group' rules to make them union-like vs intersecting-like (possibly) or maybe just to group them for reuse in other profiles. This raises the question of identifying profiles, so lets save that for another issue. I presume that the grouping of the Particular Variation is to provide a way of representing co-occurring particulars that are not able to be represented with the Haplotype, Genotype concepts which are constrained to grouping around a single instance of a sequence (or reference molecule, chr 1, transcript x, protein y, etc..). Again, any real world examples with notes on how common they are would be very helpful in clarifying this portion of the model.

We discussed on call today, but to document our progress:

Yes, mixed cases between the types definitely do happen. One such example is the ALK fusion G1202R co-mutation. Here we see a rule-based variation (ALK fusion) co-mutated with a specific variation (G1202R mutation).

I think we should abandon the self-referential behavior of VPs, as that was really to try and capture variation sets, which we've now modeled separately (and better) as equivalencesets/expansionsets.

I. 'Sequence-Level Variation' vs 'Post-Sequence Variation' (original names)

I think "sequence variation" is a good name, more issues I have with the "post-sequence variation".
It's partly a "causation and correlation" issue any sequence variation can potentially cause a post-sequence variation but due to the complexity of a cell we still don't really understand this effect. What I want to say is that maybe "variation" is not the best word here. The "sequence variation" comes from the observed difference to a reference sequence a kind of "global" standard. For expression or epigenetics it's still more complicated, e.g. for expression we would assume that there is a standard for the specific tissue type or even cell type and a significant difference was measured. In expression often "n-fold" is used as a term, so maybe "measured change" or "measured difference" or "fold change" would be potential candidates?
Probably I also didn't fully understood yet what we want to include exactly in the "post-sequence variation".

II. 'Precise Variation' vs 'Bucket Variation' (original names)

what about just
"variation" and "variation class"
what I struggle with are the many "any"s

These can define classes of 'sequence-level variation', e.g. "any deletion spanning exon 3 of the EGFR gene", "any fusion between the BRAF and CUL1 genes", "any frameshift mutation in the first two exons of the BRCA2 gene", "any activating mutation in the KRAS gene", "any variation resulting in amplification of the ALK gene"

it's more or less saying "we don't know but this is the change we measured". So we could also just name It "measured change" or "measured difference" since we don't know if a mutation which activates the KRAS gene even is in the KRAS gene itself, right? Also here I am afraid that the data-model might imply  causation which is not really there. I also struggle with a precise difference between "post-sequence-variation" and "bucket variation".
I hope I don't create too much confusion with my input and it is somehow helpful.

Thanks @GideonGiao. 👍 to your comments about "post-sequence variation". I don't think we've set any of these terms in stone, and this is also one that I think doesn't precisely capture the meaning of the concept. Other terms we've considered include "other molecular variation", which is a bit more of a catch-all and doesn't imply a temporal ordering.
re: point 2:

II. 'Precise Variation' vs 'Bucket Variation' (original names)

Our model currently calls these "particular variation" and "rule-based variation", which are both members of the "variation" superclass. While it's definitely a different way of thinking about variation, the need for "any" in these statements is born out of generalization more than imprecision. Specifically, rule-based variation is needed when a cohort study describes patients with certain shared molecular characteristics, but they do not necessarily observe only one variation that matches those characteristics. These types of statements are very common in the interpretation of somatic variation in cancers, for instance.

Thank you @ahwagner  for your response. I agree with you that a more imprecise term for a "rule-based variation" is required. I worked for 6 years at the cancer research center in germany and everything there is related to cancer, since I also worked a lot with biologist and other bioinformatician I can only say that the word "variation" is most of the time direclty connected with a molecular change in a sequence at least that is my experience. I don't see a issue with changing that over time. Maybe for now we also want to consider words like "difference" or "change" instead of variation. Describing a shared property of a cohort of patients is quite tricky. I know I might come across quite picky. I only try to avoid confusion later on when we will use this model in different resarch fields.


[question] Position: fixed

Hi,
is there a reason why you set the position attribute to fixed and not e.g. relative?

Yes,
It helps for variety of calculation

so it would be a bad idea to set it to position: relative at the moment?

Some of the features might not work as expected

okay. thanks for the reply :)


Bumb StakingBrain image version

Rationale:
https://github.com/dappnode/DNP_DAPPMANAGER/issues/1803#issuecomment-1903935622

Closed by https://github.com/dappnode/DAppNodePackage-web3signer-gnosis/pull/83


Maintenance Pages App Tidy Up

There is a bunch of all maintenance pages that are no longer require. These may the solution look more complicated and should be removed.

Unused pages removed


Problem with the Counter DSL - name property

Im not able to set the reference name for the counter as its being taken for the class name.
here is my code: -
 def my_method(test_plan:, counter_ref_name:, range: )
    test_plan.counter name: counter_ref_name,
                      start: range[:start],
                      end:  range[:end],
                      incr: '1',
                      format: '0000' do
    end

generated jmx counter -
  <CounterConfig enabled="true" guiclass="CounterConfigGui" testclass="CounterConfig" testname="skc">
          <stringProp name="CounterConfig.start">1</stringProp>
          <stringProp name="CounterConfig.end">9999</stringProp>
          <stringProp name="CounterConfig.incr">1</stringProp>
           <stringProp name="CounterConfig.name"/>
          <stringProp name="CounterConfig.format">0000</stringProp>
          <boolProp name="CounterConfig.per_user">true</boolProp>
          <boolProp name="CounterConfig.reset_on_tg_iteration">true</boolProp>
        </CounterConfig

It appears like the 'name' param is being taken by the testname in the update params helper method and deleted from the params, so the update at xpath can't find the param 'name' anymore.

Perhaps the reference name can be set to always be the same as the name


fix(oxc_parser) correct span for decorators

Preserve span position when decorators are eaten. For example:
@dec1 class A {}

should be parsed into a ClassDeclaration with start = 0(before @dec1) rather than start = 6(after @dec1).
It's not clear to me how to handle decorators before export. Tried to run it in ast explorer but their babel and swc don't support it now, I preserved the original behavior to the best degree.
@dec1 export class A {}

will have a ModuleDeclaration starting at 0 but the ClassDeclaration would start at the class keyword. It would contain a decorator that starts at 0 though.

lol there's an option for this.

@Boshen Thank you for pointing me in the right direction! Babel seems to think the ExportNamedDeclaration starts after the decorator but the ClassDeclaration within it starts at the decorator.

Babel seems to think the ExportNamedDeclaration starts after the decorator but the ClassDeclaration within it starts at the decorator.

Maybe because decorators are always transpiled. Let's stick with babel for now.

Babel seems to think the ExportNamedDeclaration starts after the decorator but the ClassDeclaration within it starts at the decorator.

Maybe because decorators are always transpiled. Let's stick with babel for now.

Yes we currently align with babel.

FYI you can still look at the benchmarks here

Thank you! This'll make our diagnostics look better for the linter.


add REPO as key in all db tables

?
also see https://github.com/larshp/abapGitServer/issues/30
add migration program?
or not, it will add another key field to eg obj objects
add program to delete orphaned objects?

prereq for https://github.com/larshp/abapGitServer/issues/46


Boot Loops at Radio Reset

Extracted from the closed issue where I had issues compiling (now resolved using esphome command line).
I am getting boot loops still and have tried 2x ESP32s and CC1101 modules and followed the wiring meticulously.  The manufacturer has confirmed the pin outs are as printed on the board and I've checked continuity between the ESP and the module.
I have enabled verbose logging and the ESP32 boots fine up until it reports SPI OK (just before radio reset) and then it reboots.
Has anyone got a link to a reliable source for the CC1101 radio, as I have tried two variants and I'm not convinced that the pin outs documented are accurate, so I am not sure if I have fried them by following the supplied pin outs, which the manufacturer has subsequently said are different
Here's the ESP logs in case they help with identifying the root cause:
[14:13:56]SDK:2.2.2-dev(38a443e)/Core:3.1.2=30102000/lwIP:STABLE-2_1_3_RELEASE/glue:1.2-65-g06164fb/BearSSL:b024386
[14:13:56][I][logger:034]: Log initialized
[14:13:56][I][app:029]: Running through setup()...
[14:13:56][V][app:030]: Sorting components by setup priority...
[14:13:56][D][number:012]: 'iBoost Manual Boost Time': Sending state 15.000000
[14:13:56][C][wifi:047]: Setting up WiFi...
[14:13:56][C][wifi:060]: Starting WiFi...
[14:13:56][C][wifi:061]:   Local MAC: A0:20:A6:22:C6:A3
[14:13:56][V][wifi_esp8266:061]: Enabling STA.
[14:13:56]mode : sta(a0:20:a6:22:c6:a3)
add if0
[V][wifi_esp8266:556]: Event: Changed Mode old=OFF new=STA
[14:13:56]wifi evt: 8
nul mode, fpm auto sleep set:enalbe
sleep disable
[D][wifi:481]: Starting scan...
[14:13:56][W][component:157]: Component wifi set Warning flag: scanning for networks
[14:13:56]scandone
[D][wifi:496]: Found networks:
[14:13:56][I][wifi:539]: - 'Sunnydene2.4' [redacted]▂▄▆█
[14:13:56][D][wifi:541]:     Channel: 13
[14:13:56][D][wifi:542]:     RSSI: -65 dB
[14:13:56][I][wifi:539]: - 'Sunnydene2.4' [redacted]▂▄▆█
[14:13:56][D][wifi:541]:     Channel: 13
[14:13:56][D][wifi:542]:     RSSI: -65 dB
[14:13:56][I][wifi:539]: - 'Sunnydene2.4' [redacted]▂▄▆█
[14:13:56][D][wifi:541]:     Channel: 13
[14:13:56][D][wifi:542]:     RSSI: -73 dB
[14:13:56][I][wifi:539]: - 'Sunnydene2.4' [redacted]▂▄▆█
[14:13:56][D][wifi:541]:     Channel: 13
[14:13:56][D][wifi:542]:     RSSI: -76 dB
[14:13:56][I][wifi:539]: - 'Sunnydene2.4' [redacted]▂▄▆█
[14:13:56][D][wifi:541]:     Channel: 13
[14:13:56][D][wifi:542]:     RSSI: -83 dB
[14:13:56][D][wifi:544]: - [redacted] [redacted]▂▄▆█
[14:13:56][D][wifi:544]: - [redacted] [redacted]▂▄▆█
[14:13:56][D][wifi:544]: - [redacted] [redacted]▂▄▆█
[14:13:56][D][wifi:544]: - [redacted] [redacted]▂▄▆█
[14:13:56][I][wifi:312]: WiFi Connecting to 'Sunnydene2.4'...
[14:13:56][V][wifi:314]: Connection Params:
[14:13:56][V][wifi:315]:   SSID: 'Sunnydene2.4'
[14:13:56][V][wifi:318]:   BSSID: DC:39:6F:72:EF:05
[14:13:56][V][wifi:348]:   Password: [redacted]
[14:13:56][V][wifi:353]:   Channel: 13
[14:13:56][V][wifi:362]:   Using DHCP IP
[14:13:56][V][wifi:364]:   Hidden: NO
[14:13:56][V][wifi_esp8266:514]: Event: Changed AuthMode old=OPEN new=WPA2 PSK
[14:13:56]wifi evt: 2
scandone
state: 0 -> 2 (b0)
state: 2 -> 3 (0)
state: 3 -> 5 (10)
add 0
aid 7
cnt

connected with Sunnydene2.4, channel 13
dhcp client start...
[V][wifi_esp8266:490]: Event: Connected ssid='Sunnydene2.4' bssid=DC:39:6F:72:EF:05 channel=13
[14:13:56]wifi evt: 0
ip:<IP_ADDRESS>,mask:<IP_ADDRESS>,gw:<IP_ADDRESS>
[V][wifi_esp8266:529]: Event: Got IP static_ip=<IP_ADDRESS> gateway=<IP_ADDRESS> netmask=<IP_ADDRESS>
[14:13:56]wifi evt: 3
[I][wifi:616]: WiFi Connected!
[14:13:56][C][wifi:427]:   Local MAC: A0:20:A6:22:C6:A3
[14:13:56][C][wifi:432]:   SSID: [redacted]
[14:13:56][C][wifi:435]:   IP Address: <IP_ADDRESS>
[14:13:56][C][wifi:438]:   BSSID: [redacted]
[14:13:56][C][wifi:440]:   Hostname: 'iboost32'
[14:13:56][C][wifi:442]:   Signal strength: -69 dB ▂▄▆█
[14:13:56][V][wifi:444]:   Priority: 0.0
[14:13:56][C][wifi:446]:   Channel: 13
[14:13:56][C][wifi:447]:   Subnet: <IP_ADDRESS>
[14:13:56][C][wifi:448]:   Gateway: <IP_ADDRESS>
[14:13:56][C][wifi:449]:   DNS1: <IP_ADDRESS>
[14:13:56][C][wifi:450]:   DNS2: <IP_ADDRESS>
[14:13:56][D][wifi:625]: Disabling AP...
[14:13:56][C][api:025]: Setting up Home Assistant API server...
[14:13:56]SPI OK
[14:13:56][W][iBoost:113]: SPI OK
[14:13:56]
--------------- CUT HERE FOR EXCEPTION DECODER ---------------

[14:13:56]Soft WDT reset
[14:13:56]
[14:13:56]Exception (4):
[14:13:56]epc1=0x40100765 epc2=0x00000000 epc3=0x00000000 excvaddr=0x00000000 depc=0x00000000
[14:13:56]
[14:13:56]>>>stack>>>
[14:13:56]
[14:13:56]ctx: cont
[14:13:56]sp: 3ffffcf0 end: 3fffffd0 offset: 0160
[14:13:56]3ffffe50:  40201094 3ffefc18 3ffefa7c 4020109e
[14:13:56]3ffffe60:  00000000 3ffefc18 3ffefa7c 40211b76
[14:13:56]3ffffe70:  3fff164c 00000008 3ffef960 402102bd
[14:13:56]3ffffe80:  00000006 00000006 3fff20fc 40100d36
[14:13:56]3ffffe90:  00000102 00000014 00000005 3fff1cdc
[14:13:56]3ffffea0:  3fff1bf4 00000020 3fff151c 3fff1cdc
[14:13:56]3ffffeb0:  3fff1bf4 3ffefa88 3fffff64 40213918
[14:13:56]3ffffec0:  00000000 feefeffe feefeffe feefeffe
[14:13:56]3ffffed0:  40227188 00000000 7fc00000 00000000
[14:13:56]3ffffee0:  3fff1b14 3fff1b18 3fff1b18 00000000
[14:13:56]3ffffef0:  3ffffef8 0000000d 78656c41 65646e61
[14:13:56]3fffff00:  61334272 00000072 00000000 00000000
[14:13:56]3fffff10:  00000000 00000000 00000000 00000000
[14:13:56]3fffff20:  00000000 00000000 00000000 40227188
[14:13:56]3fffff30:  00000000 7fc00000 00000000 3fff15f4
[14:13:56]3fffff40:  3fff15f8 3fff15f8 40227150 00000000
[14:13:56]3fffff50:  7fc00000 00000000 3fff1acc 3fff1aec
[14:13:56]3fffff60:  3fff1aec 3fff1524 3fff1528 3fff1528
[14:13:56]3fffff70:  a5a5a500 3fffff84 00000001 feefeffe
[14:13:56]3fffff80:  feefeffe 3fff1ddc feefeffe feefeffe
[14:13:56]3fffff90:  3fff1d24 00000000 3fff1bbc feefeffe
[14:13:56]3fffffa0:  feefeffe feefeffe feefeffe 3ffefe28
[14:13:56]3fffffb0:  3fffdad0 00000000 3ffefdfc 40222430
[14:13:56]3fffffc0:  feefeffe feefeffe 3fffdab0 40100465
[14:13:56]<<<stack<<<
[14:13:56]
--------------- CUT HERE FOR EXCEPTION DECODER ---------------

[14:13:56] ets Jan  8 2013,rst cause:2, boot mode:(3,6)
[14:13:56]
[14:13:56]load 0x4010f000, len 3424, room 16
[14:13:56]tail 0
[14:13:56]chksum 0x2e
[14:13:56]load 0x3fff20b8, len 40, room 8
[14:13:56]tail 0
[14:13:56]chksum 0x2b
[14:13:56]csum 0x2b
[14:13:56]v0006a7a0
[14:13:56]~ld

I can't comment on reliability of supplier in general. But I can say that I bought two from this seller last December, and they worked.
https://www.ebay.co.uk/str/cayin35
More recently I bought two more from this seller, and they worked.
https://www.ebay.co.uk/str/alimodule
I don't think either came with pinout definition, so I just assumed they matched the diagram here:
https://github.com/JNSwanson/ESP-Home-iBoost

Thank you!
Something like this one OK and we're the pins as per the board?
ebay

This one
cayin
and this one
alimodule

This one
cayin
and this one
alimodule

Many thanks - I had been using the 433 boards which are supposedly tuneable to 868.  I'll give these a whirl.
Could you confirm your pin outs used matched what I've found here when you get a moment please?

I followed the labelling here which seems the same as your image except it has CLK in place of your SCLK

### SUCCESS with the new board!
Thank you for your help @srchild .  I've got poor reception, so now tweaking the frequency as per the instructions, but at least I'm up and running :)


Environment Error - mmcv version mismatch.

when trying to tun test.py, on line 14:
import mmdet
I get the following error:
AssertionError: MMCV==1.5.3 is used but incompatible. Please install mmcv>=2.0.0rc4, <2.2.0.
My installed mmdet version is 2.25.1 as mentioned in the install.md page.
Does anyone else encountered this issue?

Can I see your pip list?

I reinstalled all of the packages and it fixed the issue.
Thank you for the quick reply!


Pass target attribute to icon button when button label is hidden at breakpoint

This pull request is a fix for problem described in #11986
Description
Adding the target attribute to <x-filament::button /> component when labeledFrom is passed
Visual changes

Functional changes

[ ] Code style has been fixed by running the composer cs command.
[ ] Changes have been tested to not break existing functionality.
[ ] Documentation is up-to-date.

Thanks, @wallacemaxters!
Please make sure to check all checkboxes next time.


Allow flow_manager to remove flow in a disabled switch

The NApps 'of_lldp' and 'of_l2ls' needs remove their installed flows once a switch is disabled. This change is necessary to allow the mentioned NApps install and remove flows using "flow_manager".

Related https://github.com/kytos/of_lldp/issues/55


⚠ GitLab Server has degraded performance

In 87a95c0, GitLab Server (https://gitlab01.its-telekom.eu) experienced degraded performance:

HTTP code: 200
Response time: 9284 ms

Resolved: GitLab Server performance has improved in d84a374.