Segmentation fault on cythonizing

We are trying to cythonize our code (github.com/tardis-sn/tardis) within our TRAVIS environment and we get a segmentation fault during the cythonizing (cython 0.27.3 and 0.28) step (see https://travis-ci.org/tardis-sn/tardis/jobs/362581597).
Here's the log:
Compiling tardis/montecarlo/montecarlo.pyx because it changed.
[1/1] Cythonizing tardis/montecarlo/montecarlo.pyx
/home/travis/.travis/job_stages: line 57:  4789 Segmentation fault      (core dumped) CC=$COMPILER python setup.py $SETUP_CMD

I'm also pinging @unoebauer as he was helping to debug this problem

@scoder we tried - again segfault: https://travis-ci.org/tardis-sn/tardis/jobs/365640859 -
it downloads this wheel:
Downloading https://files.pythonhosted.org/packages/f7/a1/0ecf3ace2e97eaf63f93931be38361763fff0118aca6b70119dde9867e14/Cython-0.28-cp27-cp27mu-manylinux1_x86_64.whl

Do I understand correctly that you cannot reproduce this locally, but only on travis?
I tried compiling that .pyx file myself and (unsurprisingly) couldn't get it to crash. And the file looks rather unsuspicious, definitely not something that could run into resource limits or so.
Ok, travis uses an old Ubuntu version, but apart from that, it's entirely non-obvious to me what might trigger a crash here. I've never seen something like this in years. But I admit that I also don't remember seeing anyone use conda on travis yet.

@scoder I've seen many people use conda on TRAVIS - but I have not seen that bug. Not sure where it comes from as we also can not reproduce it locally. I filed a bug on TRAVIS - maybe they can help.

@scoder - I think we are getting close. TRAVIS's @BanzaiMan gave me access to the debug mode and I got a core dump:
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f17a0579ea4 in _PyObject_GetDictPtr () from /home/travis/miniconda/envs/tardis/bin/../lib/libpython2.7.so.1.0

@scoder I've used the cython master in this build and it still crashes: https://travis-ci.org/tardis-sn/tardis/jobs/381891389

python setup.py build_ext -D CYTHON_CLINE_IN_TRACEBACK=0
produced this error:
[ 6/13] Cythonizing /home/travis/cython/Cython/Compiler/Pythran.py
[ 7/13] Cythonizing /home/travis/cython/Cython/Compiler/Scanning.py
[ 8/13] Cythonizing /home/travis/cython/Cython/Compiler/Visitor.py
[ 9/13] Cythonizing /home/travis/cython/Cython/Plex/Actions.py
[10/13] Cythonizing /home/travis/cython/Cython/Plex/Scanners.py
[11/13] Cythonizing /home/travis/cython/Cython/Runtime/refnanny.pyx
[12/13] Cythonizing /home/travis/cython/Cython/StringIOTree.py
[13/13] Cythonizing /home/travis/cython/Cython/Tempita/_tempita.py
building 'Cython.Plex.Scanners' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/home
creating build/temp.linux-x86_64-2.7/home/travis
creating build/temp.linux-x86_64-2.7/home/travis/cython
creating build/temp.linux-x86_64-2.7/home/travis/cython/Cython
creating build/temp.linux-x86_64-2.7/home/travis/cython/Cython/Plex
gcc -pthread -B /home/travis/miniconda/envs/tardis/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DCYTHON_CLINE_IN_TRACEBACK=0=1 -I/home/travis/miniconda/envs/tardis/include/python2.7 -c /home/travis/cython/Cython/Plex/Scanners.c -o build/temp.linux-x86_64-2.7/home/travis/cython/Cython/Plex/Scanners.o
/home/travis/cython/Cython/Plex/Scanners.c: In function ‘__Pyx_AddTraceback’:
<command-line>:0:28: error: lvalue required as left operand of assignment
/home/travis/cython/Cython/Plex/Scanners.c:1465:53: note: in expansion of macro ‘CYTHON_CLINE_IN_TRACEBACK’
 #define __Pyx_CLineForTraceback(tstate, c_line)  (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
                                                     ^
/home/travis/cython/Cython/Plex/Scanners.c:11195:18: note: in expansion of macro ‘__Pyx_CLineForTraceback’
         c_line = __Pyx_CLineForTraceback(tstate, c_line);
                  ^
error: command 'gcc' failed with exit status 1

I meant something like CFLAGS="$CFLAGS -D CYTHON_CLINE_IN_TRACEBACK=0".

@scoder that worked  - it doesn't crash. What's the best way to get this into the travis version?

@scoder we integrated this into travis in the following way: https://github.com/tardis-sn/tardis/blob/master/.travis.yml (using the compile flags). At what point can we use a standard release version of cython again?

Hmm, looks like the fix didn't make it into the changelog. It's included in 0.28.3, though.

@scoder - it still crashes https://travis-ci.org/tardis-sn/tardis/jobs/405443747


lbmap: Guarantee order of backends while scaling service

This change is

Runtime failures seem potentially related:
21:38:50 Summarizing 7 Failures:
21:38:50
21:38:50 [Fail] RuntimeLB [It] validates basic service management functionality
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:92
21:38:50
21:38:50 [Fail] RuntimeLB With Containers [It] validates that services work for L3 (IP) loadbalancing
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:189
21:38:50
21:38:50 [Fail] RuntimeLB With Containers [It] validates that services work for L4 (IP+Port) loadbalancing
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:264
21:38:50
21:38:50 [Fail] RuntimeLB With Containers [It] validates service recovery on restart
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:290
21:38:50
21:38:50 [Fail] RuntimeLB Services Policies [It] tests with conntrack enabled
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:391
21:38:50
21:38:50 [Fail] RuntimeLB Services Policies [It] tests with conntrack disabled
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:391
21:38:50
21:38:50 [Fail] RuntimeLB Services Policies [It] tests with service performing L4 port mapping
21:38:50 /home/jenkins/workspace/Cilium-PR-Ginkgo-Tests-Validated/src/github.com/cilium/cilium/test/runtime/lb.go:376

Runtime failures seem potentially related:

It is related. It was an uninitialized map.

test-me-please

test-me-please


curl: 8.4.0 -> 8.5.0

Automatic update generated by nixpkgs-update tools. This update was made based on information from https://repology.org/project/curl/versions.
meta.description for curl is: A command line tool for transferring files with URL syntax
meta.homepage for curl is: https://curl.se/
meta.changelog for curl is: https://curl.se/changes.html#8_5_0
Updates performed

Version update

To inspect upstream changes
Impact

Checks done (click to expand)

built on NixOS
Warning: a test defined in passthru.tests did not pass
found 8.5.0 with grep in /nix/store/41xjs6ssq20w37na9mq23jyvyazmafd6-curl-8.5.0-bin
found 8.5.0 in filename of file in /nix/store/41xjs6ssq20w37na9mq23jyvyazmafd6-curl-8.5.0-bin

Rebuild report (if merged into master) (click to expand)

48118 total rebuild path(s)

48118 package rebuild(s)

First fifty rebuilds by attrpath

ArchiSteamFarm
BeatSaberModManager
CHOWTapeModel
ChowCentaur
ChowKick
ChowPhaser
CuboCore.coreaction
CuboCore.corearchiver
CuboCore.corefm
CuboCore.coregarage
CuboCore.corehunt
CuboCore.coreimage
CuboCore.coreinfo
CuboCore.corekeyboard
CuboCore.corepad
CuboCore.corepaint
CuboCore.corepdf
CuboCore.corepins
CuboCore.corerenamer
CuboCore.coreshot
CuboCore.corestats
CuboCore.corestuff
CuboCore.coreterminal
CuboCore.coretime
CuboCore.coretoppings
CuboCore.coreuniverse
CuboCore.libcprime
CuboCore.libcsys
DisnixWebService
EBTKS
EmptyEpsilon
Fabric
HentaiAtHome
LAStools
LASzip
LASzip2
LibreArp
LibreArp-lv2
Literate
MIDIVisualizer
MMA
NSPlist
OSCAR
OVMF
OVMFFull
PageEdit
PlistCpp
QuadProgpp
R

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/41xjs6ssq20w37na9mq23jyvyazmafd6-curl-8.5.0-bin \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A curl https://github.com/r-ryantm/nixpkgs/archive/7be9f0f52630eec0bd9026ff0e0e31c8116ac7b2.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/7be9f0f52630eec0bd9026ff0e0e31c8116ac7b2#curl

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/41xjs6ssq20w37na9mq23jyvyazmafd6-curl-8.5.0-bin
ls -la /nix/store/41xjs6ssq20w37na9mq23jyvyazmafd6-curl-8.5.0-bin/bin

Pre-merge build results
NixPkgs review skipped

Maintainer pings
cc @lovek323 for testing.

There are 2 known vulnerabilities in 8.4.0: https://curl.se/docs/vuln-8.4.0.html

Builds on aarch64-{darwin,linux}, x86_64-{darwin,linux}.

@ofborg eval


Support for Displays, Ideas!

desperately need ability to display sensor values , create naming structure for values
battery level
wifi connection indication, signal strength, SSID
display graph of sensor values
error log display?


Prohibit information loss

1.) Connection lost Message:
"You have lost connection to the 4Minitz server.
You will lose unsaved data if you close your browser.
Click icon for reconnection attempt.
If problem persist, contact server admin."

[ ]  Check usability on smartphone!

2.) Use window.onbeforeunload()
See http://stackoverflow.com/a/1704783/2580805
message: "Do you really want to leave 4Minitz?"

Team estimation: 1d (or less)


docs: fix wrong demo code

Summary

修改文档中的错误示例代码
Details

🤖 Generated by Copilot at 4f50ece

Add a new section of FAQs to the routes guide in English and Chinese, explaining how to compile react-router packages to es5 for compatibility (link, link)
Fix a typo in the heading level of the FAQs section in the Chinese version of routes.mdx (link)
Update the code snippet in the Chinese version of routes.mdx to include the defineConfig export statement (link)

Related Issue

Checklist

[x] I have added changeset via pnpm run change.
[x] I have updated the documentation.
[x] I have added tests to cover my changes.

This part of the documentation should be removed,  because react-router has been added to "source.include".

This part of the documentation should be removed, because react-router has been added to "source.include".

Indeed, this FAQ is outdated and should be removed.


Fix typo in the UiController

Task Description
Fix the typo in intexWithRoute to indexWithRoute:
public class UiController implements ErrorController
{

    @GetMapping(path = { "/**", "/error" }, produces = { MediaType.TEXT_HTML_VALUE })
    public String intexWithRoute(HttpServletResponse response)

Help

Our chat
Points of contact:

@carlspring
@sbespalov
@fuss86

Hi, I'd like to take this up.

Go for it!


SILOptimizer: move String concatination optimization from SILCombine/ConstantFolding to StringOptimization.

This simplifies some code and it's not required to try this optimization on every run of SILCombine and ConstantPropagation.

@swift-ci test

@swift-ci benchmark

Performance: -O

Regression
OLD
NEW
DELTA
RATIO

Data.append.Sequence.64kB.Count
25
29
+16.0%
0.86x (?)

Improvement
OLD
NEW
DELTA
RATIO

CharIteration_korean_unicodeScalars
3120
2800
-10.3%
1.11x (?)

CharIndexing_ascii_unicodeScalars
3840
3520
-8.3%
1.09x

CharIteration_japanese_unicodeScalars
4040
3720
-7.9%
1.09x (?)

CharIteration_punctuatedJapanese_unicodeScalars
560
520
-7.1%
1.08x (?)

CharIteration_chinese_unicodeScalars
2400
2240
-6.7%
1.07x (?)

Code size: -O
Performance: -Osize

Regression
OLD
NEW
DELTA
RATIO

FlattenListLoop
1204
1530
+27.1%
0.79x (?)

Improvement
OLD
NEW
DELTA
RATIO

DataCreateMedium
6200
4000
-35.5%
1.55x

CharIteration_russian_unicodeScalars_Backwards
4120
3520
-14.6%
1.17x

CharIteration_japanese_unicodeScalars_Backwards
6400
5480
-14.4%
1.17x

CharIteration_korean_unicodeScalars_Backwards
5040
4320
-14.3%
1.17x

CharIteration_chinese_unicodeScalars_Backwards
3680
3160
-14.1%
1.16x (?)

CharIteration_punctuatedJapanese_unicodeScalars_Backwards
960
840
-12.5%
1.14x

CharIndexing_punctuatedJapanese_unicodeScalars_Backwards
1640
1440
-12.2%
1.14x (?)

FlattenListFlatMap
4081
3604
-11.7%
1.13x (?)

CharIndexing_japanese_unicodeScalars_Backwards
10440
9400
-10.0%
1.11x (?)

CharIteration_punctuated_unicodeScalars_Backwards
840
760
-9.5%
1.11x

CharIndexing_chinese_unicodeScalars_Backwards
6520
5920
-9.2%
1.10x (?)

DataAccessBytesMedium
59
54
-8.5%
1.09x (?)

CharIndexing_ascii_unicodeScalars_Backwards
7120
6560
-7.9%
1.09x (?)

CharIndexing_tweet_unicodeScalars_Backwards
14000
12920
-7.7%
1.08x (?)

CharIndexing_russian_unicodeScalars_Backwards
7480
6920
-7.5%
1.08x (?)

CharIndexing_punctuated_unicodeScalars_Backwards
1800
1680
-6.7%
1.07x (?)

Code size: -Osize
Performance: -Onone
Code size: -swiftlibs

How to read the data
The tables contain differences in performance which are larger than 8% and
differences in code size which are larger than 1%.
If you see any unexpected regressions, you should consider fixing the
regressions before you merge the PR.
Noise: Sometimes the performance results (not code size!) contain false
alarms. Unexpected regressions which are marked with '(?)' are probably noise.
If you see regressions which you cannot explain you can try to run the
benchmarks again. If regressions still show up, please consult with the
performance team (@eeckstein).

Hardware Overview
  Model Name: Mac mini
  Model Identifier: Macmini8,1
  Processor Name: 6-Core Intel Core i7
  Processor Speed: 3.2 GHz
  Number of Processors: 1
  Total Number of Cores: 6
  L2 Cache (per Core): 256 KB
  L3 Cache: 12 MB
  Memory: 64 GB


Please update cocoapod for this awsome framework

Cocoapod  still not support swift 3

I am using Xcode8 Swift3 got a lot of errores?


HUNTER_CONFIGURATION_TYPES

Upgrade current Release/Debug-only build of download scheme. Read the global variable (toolchain) HUNTER_CONFIGURATION_TYPES (See CMAKE_CONFIGURATION_TYPES).
Example:

Allow Release-only build
combination HUNTER_BUILD_SHARED_LIBS=ON and HUNTER_CONFIGURATION_TYPES=Release is the same as "regular" package managers: less size, less build (more libraries compatible with each other), fast
Allow customization:
Release, Debug, RelWithDebInfo, RelMinSize
User-defined types

Create one build scheme url_sha1_cmake.cmake.in (?) instead of two url_sha1_release_debug.cmake.in url_sha1_combined_release_debug.cmake.in.

Done, e.g. v0.9.1


emulated_hue does not support changing colours of lights

Make sure you are running the latest version of Home Assistant before reporting an issue.
You should only file an issue if you found a bug. Feature and enhancement requests should go in the Feature Requests section of our community forum:
Home Assistant release (hass --version):
0.42.3
Component/platform:
emulated_hue
Description of problem:
The emulated hue platform does not allow the changing of light colours.
This is now supported on Alexa, once support is added to the hue emulation component we should be able to control light colours.

You should only file an issue if you found a bug. Feature and enhancement requests should go in the Feature Requests section of our community forum:


Add img for rst

Integrate https://hub.docker.com/r/danielsiepmann/t3-sphinx/ for rendering documentation

As helper, while writing your extension documentation? I think I could also include it to the clitools. Anything like ct typo3:docrender ? Would that also help?

Ask the author, imo he is active in the doc team and on slack what the best way would be.
Imo CT is optional  cause rendering ist triggered while writing with the doc extensions by Xavier

Relates to #123


auth: mobile/password signup payload is missing country_code

https://docs.hasura.io/0.15/manual/users/mobile_password.html

Fixed in d60731f662ca2db0fef536ad219409ce0fcd647c


Pitts -> Jones

Pull Request Test Coverage Report for Build 438

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 68.487%

Totals

Change from base Build 436:
0.0%

Covered Lines:
928

Relevant Lines:
1355

💛  - Coveralls


Look for modified APIs in sysservicedb

Originally, I didn't expect OEMs to actually change arguments or return values of system service APIs, but I just confirmed that multiple OEMs do this, so I need to start checking for this.
I may change the output slightly, so that additions and changes are distinguished. I'm thinking:

[+] for added
[!] for changed

Added: https://github.com/jakev/dtfmods-core/commit/7ae4f6136653c2799ea47e56a1eb2f87873e401d


Add support for backports repos

If -backports=true is provided to any of the publish subcommands, the
published repo will have the lines
NotAutomatic: yes
ButAutomaticUpgrades: yes
in its Release file, which is necessary when creating or mirroring a
backports repo -- the repo should be available, but apt should not
choose packages in that repo by default. This flag can be later unset
with -backports=false.
This isn't a complete fix for #184 since we don't capture all the
fields, but it solves the most common use case.

The test failures appear to be because squeeze and squeeze-lts don't exist any more as of a few days ago....
Also I guess I should add test coverage and documentation, but Go is new to me and I don't quite follow the test framework.

Hey @smira, is this a reasonable approach to solving this? Would you like me to write docs and try to figure out how to write tests?

@geofft docs is something which is missing.
I should have fixed all the squeeze failures in system tests.
In short, you can launch whole test suite by running:
make system-test
This would do one-time pull for fixtures and start test suite. It might take a long time to run.
So once you've pulled fixtures, you can re-build aptly with:
gom build -o $GOPATH/bin/aptly main.go
And then you can do:
system/run.py Publish
To run all the publish-related tests.
Also you can ask test runner to re-capture expected output on failures with:
system/run.py --capture Publish

I can take a look at system tests this week, I'm still trying to keep up with my pending queue :(

I think this is a suboptimal solution. What aptly should do is to stop stripping NotAutomatic/ButAutomaticUpgrades fields from the remote repo Release file, and thus preserve them throughout the mirror/snapshot/publish chain.
with the approach proposed in this PR we need to somehow identify if we are dealing with a backport repo (grep the mirror url? code that in the mirror name? what about if a third-party repo is configured as a backport but doesnt explicitly call the repo '.backport.'?) and pass the backport=true option, which is difficult/cumbersome to script/automate and would result in manual intervention.
the even better approach for aptly would be to preserve all the extra fields from the remote Release file, except those that needs to change of course (like date, hashes, etc)

Yeah, that was the approach I initially wanted to do. The trouble is that a publish doesn't necessarily map to a single mirror. You can imagine doing something like
$ aptly mirror create main http://ftp.debian.org/debian/ jessie main
$ aptly mirror create bpo http://ftp.debian.org/debian/ jessie-backports main
$ aptly mirror update main; aptly mirror update bpo
$ aptly snapshot create main-20160405 from mirror main
$ aptly snapshot create bpo-20160405 from mirror bpo
$ aptly publish snapshot -component=main,bpo main-20160405 bpo-20160405 jessie

which converts two upstream Release files (/debian/dists/jessie/Release and /debian/dists/jessie-backports/Release) into one aptly-generated Release file (/dists/jessie/Release). What should it do in that case? And this isn't actually that weird; if you create the bpo mirror with -filter for the packages you want out of backports, it's entirely reasonable to combine them into one repo that does not have NotAutomatic: yes.
If there's a good way to handle this case, I'm happy to implement it. Maybe the best option is to give an error message if the Release files don't match in their extra configuration, and allow you to specify something on the command line (e.g. aptly publish snapshot -follow-release-file-from=main -component=main,bpo ....) I'm open to suggestions.
What other options are there in Release files besides NotAutomatic and ButAutomaticUpgrades? It'd be good to know for testing.

On Tue, Apr 5, 2016 at 3:54 PM, Geoffrey Thomas<EMAIL_ADDRESS>wrote:

Yeah, that was the approach I initially wanted to do. The trouble is that
a publish doesn't necessarily map to a single mirror. You can imagine doing
something like
$ aptly mirror create main http://ftp.debian.org/debian/ jessie main
$ aptly mirror create bpo http://ftp.debian.org/debian/ jessie-backports main
$ aptly mirror update main; aptly mirror update bpo
$ aptly snapshot create main-20160405 from mirror main
$ aptly snapshot create bpo-20160405 from mirror bpo
$ aptly publish snapshot -component=main,bpo main-20160405 bpo-20160405 jessie
which converts two upstream Release files (/debian/dists/jessie/Release
and /debian/dists/jessie-backports/Release) into one aptly-generated
Release file (/dists/jessie/Release). What should it do in that case? And
this isn't actually that weird; if you create the bpo mirror with -filter
for the packages you want out of backports, it's entirely reasonable to
combine them into one repo that does not have NotAutomatic: yes.
If there's a good way to handle this case, I'm happy to implement it.
Maybe the best option is to give an error message if the Release files
don't match in their extra configuration, and allow you to specify
something on the command line (e.g. aptly publish snapshot
-follow-release-file-from=main -component=main,bpo ....) I'm open to
suggestions.

you could

merge the options (in case of conflicting options, you might want to
error & stop)
take the intersection (so only the options present in all the release
files)
throw an error and halt the operation because maybe you are doing
something you really shouldnt

also this is a rather corner case, and while we have at hand a real users
problem (where many more have complained about it) i doubt this will be a
widespread issue, which could be resolved with a local repo for example.

What other options are there in Release files besides NotAutomatic and
ButAutomaticUpgrades? It'd be good to know for testing.

you can look it up by yourself i guess

I agree that it's a corner case, but I need to implement something for this case. (And meanwhile my code works, and nobody else has proposed another PR for solving this.) I think either merging or taking the intersection are both wrong if done silently.
What options are you interested in? My use case, and as far as I can tell, the use case of everyone else in #184, is just backports. From https://wiki.debian.org/RepositoryFormat , the other options include

No-Support-for-Architecture-all, "An optional field with a temporary and very specific usecase", and specific to how the Contents files are being generated; since aptly regenerates them, we shouldn't copy them
Valid-Until: relevant to signing, probably should be managed by aptly instead of copied from the mirror
NotAutomatic and ButAutomaticUpgrades
Acquire-By-Hash: definitely should be managed by aptly instead of copied from the mirror

so I think it actually does not make sense to copy unknown fields from the Release file, because all of them other than NotAutomatic / ButAutomaticUpgrades have meanings that don't make sense for aptly mirrors. I'll try to implement something to pick up these two flags, though.

What options are you interested in? My use case, and as far as I can tell,
the use case of everyone else in #184
https://github.com/smira/aptly/issues/184, is just backports.

the only option we are really interested in is to preserve  NotAutomatic /
ButAutomaticUpgrades if the remote repository contains them. all the other
options could remain unimplemented/undefined and addresses as someone comes
up with the requirement for it (as done in this case) and do not need to be
addressed now

What we could do is:

allow to specify any key/value pairs which would become part of Release file after publishing
automatically inherit those key/value pairs if publish is happening on a snapshot tree which has only one mirror as root source (inheriting them from mirror's Release file).

Thoughts?

On Thu, Apr 7, 2016 at 10:52 AM, Andrey Smirnov<EMAIL_ADDRESS>wrote:

What we could do is:

allow to specify any key/value pairs which would become part of
Release file after publishing
automatically inherit those key/value pairs if publish is happening
on a snapshot tree which has only one mirror as root source (inheriting
them from mirror's Release file).

would resolve the immediate issue with backports and 1. would allow for
more complex scenarios - like it

Hi everyone,
It's been nearly a year since the last comment. Is there any more progress on this?

Currently, I work around this by using the -skip-signing flag when publishing my jessie-backports mirror, modify the Release file to include the special fields, and then use gpg --sign ... manually on the Release file. It works but is not ideal.
It is true that there needs to be a better way, overall, to have better control over any fields, however this is a pretty important case that I think deserves a flag.
Better yet, make the new  -backports flag default to 'true' if the upstream Release file contains both NotAutomatic: yes and ButAutomaticUpgrades: yes, if and only if it is not manually added and set the 'false' by the user. This way, the expected thing is the default thing.

This has been superseded by #577 - thanks, @sliverc!


Publish on Open VSX Registry

In order to use this extension pack with the open-source version of VSCode, it must be published in https://open-vsx.org/

Done: https://open-vsx.org/extension/nf-core/nf-core-extensionpack


Use self-provided xcode_config target instead of relying on @local_config_xcode

Description:
With remote execution, envoy mobile spends a significant fraction
of its built time in loading/analysis phase, and specificaly, in a
7.5 minutes build, around 2.7 minutes in evaluating @local_config_xcode
which auto configures Bazel with the locally installed Xcode versions.
Since envoy mobile passes --xcode_version=12.4 in its .bazelrc, thus
requires a specific Xcode version, we can make the build significantly
faster by creating our own xcode_config target instead of relying
on Bazel's auto configuration.
Example invocation: https://envoy.cluster.engflow.com/invocation/a23bd20b-f0b9-472b-9a07-b9e5bc629b30#performance
Risk Level: low
Testing: local/CI
Docs Changes: N/A
Release Notes: N/A

/cc @ulfjack @lfpino

Looks like https://envoy.cluster.engflow.com/invocation/29b3f4f8-1fac-439b-99c1-5bd44c0e8402 took longer with this change, but I suspect that it's because of less cache hits during the build (Bazel sends the exact Xcode version in the action Proto and we intentionally only specify 12.4 instead of 12.4.0. in xcode_version so this works with both the AppStore Xcode and the dev portal Xcode which have different builder's).
Without this , Bazel spend ~3min in analysis, which this change seems to cut roughly in half.

Just approved CI run.

not sure why swift_tests fail, looks unrelated

thanks! looks like kotlin_tests_linux also flaked

Rerunning.


Add steal KeePass passwords using KeeFarce

References:

https://github.com/denandz/KeeFarce
https://keepass.info/help/kb/sec_issues.html

Closes https://github.com/fireeye/capa-rules/issues/348
Closes https://github.com/fireeye/capa-rules/issues/322

bump, would love to get this in by the end of the week


error for encrypted live channels

Hi,
I get this error when I play widevine encrypted live content in chrome. on demand videos are playing without issues. HDCP and CGMS is not enabled.
CustomEvent {isTrusted: false, srcElement: null, target: s…a.p…r.DashVideoSource, currentTarget: s…a.p…r.Player}bubbles: truecancelBubble: falsecancelable: falsecurrentTarget: shaka.player.PlayerdefaultPrevented: falsedetail: Error: The key system has restricted all video tracks.
    at shaka.player.StreamVideoSource.onKeyStatusesChange (http://vod.domain.com/newshaka/shaka-player-master/lib/player/stream_video_source.js:1069:15)
    at shaka.media.EmeManager.onKeyStatusesChange_ (http://vod.domain.com/newshaka/shaka-player-master/lib/media/eme_manager.js:675:21)message: "The key system has restricted all video tracks."stack: (...)get stack: ()set stack: ()type: "drm"__proto__: DefineError.bhconstructor: Error()arguments: nullcaller: nullcaptureStackTrace: captureStackTrace()length: 1name: "Error"prototype: DefineError.bhstackTraceLimit: 10__proto__: ()<function scope>No Scopesmessage: ""name: "Error"toString: toString()__proto__: ObjecteventPhase: 0isTrusted: falseisTrusted: falsepath: Array[0]length: 0__proto__: Array[0]returnValue: truesrcElement: nulltarget: shaka.player.DashVideoSourcetimeStamp:<PHONE_NUMBER>287type: "error"__proto__: CustomEventbubbles: (...)cancelBubble: (...)cancelable: (...)constructor: CustomEvent()currentTarget: (...)defaultPrevented: (...)detail: (...)get detail: ()eventPhase: (...)initCustomEvent: initCustomEvent()path: (...)returnValue: (...)srcElement: (...)target: (...)timeStamp: (...)type: (...)__proto__: Eventapp.onPlayerError_ @ app.js:962shaka.util.FakeEventTarget.recursiveDispatch_ @ fake_event_target.js:143shaka.util.FakeEventTarget.recursiveDispatch_ @ fake_event_target.js:156shaka.util.FakeEventTarget.dispatchEvent @ fake_event_target.js:121shaka.player.StreamVideoSource.onKeyStatusesChange @ stream_video_source.js:1072shaka.media.EmeManager.onKeyStatusesChange_ @ eme_manager.js:675
stream.js:694 Stream video/mp4: stream has started.

What can be the issue?
Regards,
Randeep

To help narrow down the problem, can you enable debug logging? You will then see the key status for each key.

How can I enable it?
I have enabled eme_logger in chrome.

You can either use the library in uncompiled mode, or you can use the library in compiled mode with debug logging by changing -D shaka.log.MAX_LOG_LEVEL=0 to -D shaka.log.MAX_LOG_LEVEL=4 in build/lib.sh before executing build/all.sh

In an uncompiled build, you can set the log level at runtime using shaka.log.setLevel().

@tdrews @joeyparrish
it was an issue related to widevine and CGMS flag. They have given me a workaround. You can internally check with them. The ticket number is 5-2916000008909.
Thanks and regards,
Randeep

Latest update is that it is related to  chrome browser.


Menu enhancements and optimizations

Status
Ready
Related Issues
fixes: link to the issue
Description

Add Featured and Premium options
Switch checkbox to toggle
Refactor filtering logic

Screenshots
Paste here any images that will help the reviewer

Do not merge yet...still testing.


Stats event listener

Have you read the FAQ and checked for duplicate open issues?
Yes
What version of Shaka Player are you using?
v2.5.9-debug
Please ask your question
Is there any event listener to listen for Stats change? Trying to implement something like "Stats for nerds" in youtube player but couldn't find a matching event listener. Any help on this?
http://v1-6-2.shaka-player-demo.appspot.com/docs/shaka.player.Stats.html

You linked to the docs for Shaka v1.  I would recommend you check the docs for v2: https://shaka-player-demo.appspot.com/docs/api/shaka.extern.html#.Stats
Depending on what stats you care about, there are several events, but in general, you could also just poll them on some reasonable interval.
A few examples from the screenshot above:

Displayed resolution - get from player.getStats() or video.currentWidth, video.currentHeight.  No event for this is offered by the browser, so you would have to poll.
Selected track (may not be displayed yet) - get from player.getTracks(), filter for .active, listen for 'adaptation' events on player.
Volume - get from video.volume, listen for 'volumechange' events on video
Connection speed - get from player.getStats().estimatedBandwidth, no event available.  This is continuously evaluated as we fetch segments, so you'd have to poll.
Buffer - get from video.buffered, no event available from the browser, so you'd have to poll

As you can see, lots of these have to be polled, and where there are events, different pieces of information change on different events.  So my recommendation would be just to poll everything.

Hi @joeyparrish, thanks for the quick reply. Do you mean to add setInterval and listen for stats using getStats()? is that what you mean by poll?

@JeffrinManovaPrabahar , yes, you can use getVariantTracks() for audio/video tracks, and getTextTracks() for captions.

Yes, that's correct.  Does this help?

Yes absolutely. Thanks.


Add Email Verification and Password Reset to signup

Hi Karl,
This is not really an issue but was wondering if you can update the sign-up page with email verification and password reset. I am trying to implement it using .sendEmailVerification(), and while it does send an email to verify, I couldn't get the next step of checking the verification before proceeding. I'll keep prodding but I'm new to this so was thinking you could make that update. Thanks!
Abenezer

Hey @AbenezerBayeh maybe in the future but I'm releasing my Instagram clone soon so that will be the focus 👍🏻

Hey @AbenezerBayeh maybe in the future but I'm releasing my Instagram clone soon so that will be the focus 👍🏻


cachebeta: upgraded task version in samples to avoid people reference…

… old task

@baywet : Thanks for your contribution! The author(s) have been notified to review your proposed change.


componentWillReceiveProps not being triggered when initialValues are changing (with enableReinitialize: true)

Are you submitting a bug report or a feature request?
Bug Report
What is the current behavior?
componentWillReceiveProps is not being fired in my form, but enableReinitialize: true is still working properly
What is the expected behavior?
If enableReinitialize: true causes the form to reinit every time the initialValues prop changes, I'd expect to be able to hook into componentWillReceiveProps et al and monitor initialValues.  Is this a matter of proxying that lifecycle event?
Sandbox Link
https://codesandbox.io/s/l5v51lj9w9 -- See SimpleForm.js, and when you click the "Regenerate initial values" button, the values are changing, but componentWillReceiveProps isn't being fired (nothing is showing up in the console after the first render)

I think I'm running into the same problem on a project that I'm working on.  I was looking at the createReduxForm code and was curious about the following section: https://github.com/erikras/redux-form/blob/165f7ffea9d338a0f7467fcb6ca381fc390ec4d5/src/createReduxForm.js#L981-L1011
It could be my misunderstanding, but it seems that in cases when the values of the form should be reset, the value of initial will always end up being set to stateInitial and not the initialValues coming from props.  I'm not familiar with this code base so I'm likely missing something and I'm currently playing around with this in my own project.
But perhaps someone familiar with this code could weigh in.


Fix maps sample

Purpose
Fix maps sample
Approach
casting to string has become a safe operation. Hence changed the code to reflect that.

Opened PR[1]. Hence closing this.
[1] https://github.com/ballerina-lang/ballerina/pull/6027


Implement MAXIV job actions

Implement all actions needed for the MAXIV workflow in v4.

@marcoleorato described the workflow in more detail.
MAXIV jobs

Create

Use Kafka for message broker

This is handled in v3 as hook on the 'jobCreated' event, but probably makes more sense as a jobaction

Only use the "public" job type; no archive/retrieve
Kafka worker updates jobs by calling PUT /api/v3/Jobs/{{jobid}} with a payload of which files were transferred to the public storage. For example body, see the tests in CI/MAXIV/MAXIVJobs.js

Update

Send an email
The request body is translated to the handlebars context by a 'jobUpdated' hook inCI/MAXIV/handleJobSideEffects.js

This is low priority for MAXIV, and didn't block them from moving to v4 already.

TODO

[ ] Implement Kafka jobAction
[ ] Allow EmailJobAction.bodyTemplate to be read from a file (default to email-templates/job-template.html)
[ ] Replicate or update backend/email-templates/job-template.html with the new data model, adding fields if required
[ ] See if handleJobSideEffects.js:sendFinishJobEmail can be implemented completely within EmailAction and handlebars


Improve testability of release workflows

During the v0.96.0 release we had some last minute issues that made us have to re-tag. The root cause was the lack of testing when implementing #429: because of it we ran into the issue in the first place and fixing it was also difficult, requiring a trial-and-error process over multiple PRs (see #493, #494 and #496).
To avoid this, it would be helpful to restructure the release process so that we can run more of it on PRs for testing. For example, we could run the prepare job  on PRs but skip the release job.
cc @TylerHelmuth @jpkrohling any thoughts?

Ya changing this workflow is hard because we use goreleaser-pro, which makes testing in forks/local harder. In the future getting access to a goreleaser-pro key would allow testing the actual release job in a fork.
We could test the prepare job of the release workflow on PRs, but if I recall correctly it is the same as the CI test job.

We could test the prepare job of the release workflow on PRs, but if I recall correctly it is the same as the CI test job.

There must be some difference, because CI was passing on PRs but the prepare job was failing on release

I have access to the key and can share the privately for testing purposes.

I'd still prefer to enforce testing in forks/locally with the key before merging any more PRs that change the release workflow.

Makes sense to also do that, though I don't see the harm in also running prepare on PRs if we can do so easily

Would we want to run actions/upload-artifact@v4 on each PR tho?

Would we want to run actions/upload-artifact@v4 on each PR tho?

I am fine running it if it has a very short lifespan (say, 24 hours). We don't run that many PRs and 24 hours is more than enough for an actual release

How about a nightly build for those ones, perhaps with a "dispatch workflow" trigger? They take a long time, and they are risky only if changed. Ensuring on a daily basis that they run, and providing a way to run them on demand would keep the risks low, while not increasing the CI time for PRs.

I like that idea.  We could tag the image with -nightly or something like that.

Hello everyone @mx-psi @jpkrohling @TylerHelmuth, I was assigned to issue #498  above, but it's dependent on #497 as it can only be done with GoReleaser Pro and the key is not readily available. Regardless, I'd love to see the implementation of it when it's done, and if I can help out with it - I'd love to. Thank you .


feat(GridForm): Allow ReactNode for GridForm Radio label

Overview

Change type of label for Radio item in GridForm from string to ReactNode.

Closing #1785 to go with this implementation instead.
PR Checklist

[x] Related to designs: updated Profile Edit form figma
[x] Related to JIRA ticket: EGG-1266
[x] I have run this code to verify it works
[ ] This PR includes unit tests for the code change

📬Published Alpha Packages:@codecademy/gamut-kit@0.4.1-alpha.dfc7e0.0@codecademy/gamut-labs@18.3.1-alpha.dfc7e0.0@codecademy/gamut@33.2.1-alpha.dfc7e0.0<EMAIL_ADDRESS>
🚀 Styleguide deploy preview ready!https://60b00d5ffdbe6d2e4155b0ac--gamut-preview.netlify.appDeploy Logs


Deploy Kueue cluster automatically

Deploy Kueue cluster automatically during REANA deployment when the admin chooses to use Kueue in their Helm values file. Allow basic parametrisation of Kueue deployment by overriding Helm values and/or chart snippets.

Regarding kueue-related configurations like the ones I see here in the scripts directory, these should definitely be part of the REANA helm chart, and they should be created only when kueue is enabled in the settings. As an example, this is how we conditionally create ingress classes in REANA.

Done, changes are:

Add kueue parameters into the REANA helm chart
Add kueue template to deploy kueue automatically

Test
Successful kueue deployment in reana-dev with:
kind delete cluster --name kind
cd '/Users/alextintin/project/reana/src/reana'
pip install -e .
cd ~/project/reana/src
reana-dev cluster-create -m /var/reana:/var/reana --mode=debug

VERSION=v0.6.2
kubectl apply --server-side -f https://github.com/kubernetes-sigs/kueue/releases/download/$VERSION/manifests.yaml
kubectl wait --for=condition=available deployment/kueue-controller-manager -n kueue-system --timeout=5m

reana-dev cluster-build --parallel 8 --exclude-components r-a-vomsproxy -b DEBUG=1
reana-dev cluster-deploy --admin-email<EMAIL_ADDRESS>--admin-password mysecretpassword --mode=debug

Successful workflow submission
Batch Job Submission with Kueue

Job Submission with Kueue

Workflow completion

This also looks good, I just have some cosmetics comments, but they are easily reported/solved in a PR where I can comment each line separately.


Functionality to shift tab back to the previous field

Is your feature request related to a problem? Please describe.
Currently creating a form that has multiple inputs. Trying to allow to user to tab/ shift-tab back and forth throughout the fields so they do not have to use a mouse if they choose not to.
Describe the solution you'd like
The ability to press shift+tab, and have the focus be moved to the previous input field. Currently works for tabbing forward, but appears that shift+tab t move backwards is disabled by default.
Describe alternatives you've considered
Had a work around partially working but it required me to hard code what each previous field was going to be, ideally I wanted to use this generically.

Will check

This is kinda tricky to handle since the menu is not in the native HTML order, but added to the body via teleport. What I will do is handle the logic and emit the event when shift+tab is pressed. It is up to the devs to handle which element to focus afterwards.


[RF DOCS] Action Mailbox Guides

Overview
Action Mailbox is a pretty useful / interesting sub-framework of Rails, that more apps probably could benefit from. It does have a number of moving parts so I focused on explaining the flow of how things work.  I did a lot of 'in-app testing' of the docs by implementing its features in a rails app and exploring what's missing in the docs.
New sections
Here are the new things I added, in addition to clarifying the existing text.

Processing Incoming Email - more of a step by step of the flow
Mail object and it's fields
List of Inbound Email 'status' values
ActiveJobs that are part of Action Mailbox - Routing and Incineration

Testing
In addition to testing the Action Mailbox features in-app, I also ran guides:generate and guides:validate locally and got the All checked guides validate OK! output. I perused the generated html locally as well.
Follow-on Task
Moving the Ingress Configuration: the Ingress configuration section reads more like a reference/appendix to me. I think it'd make sense to move that to the end of the doc. With a smaller section with the common steps in its current place (create secure pwd, update config.action_mailbox.ingress) and then point to the bottom of the docs for details on the specific. I did not do that yet as I wanted to focus on adding the new sections first instead of moving things around.
I did test the instructions for one 'real' ingress Postmark (locally with ngrok). I did not test all the other ones (as Carlos mentioned it's be too much).

Great updates! I had one thought about a possible small addition to the routing section that may be worth mentioning, and a couple other minor bits to consider, but otherwise this LGTM. Thanks @bhumi1102!

Awesome. Thank you for the great thorough review. Looking forward to merging this to rails/rails after our 'community feedback window'.


Add Arduino-Base32 library

Proposal for a tiny library to handle Base32 decoding per rfc4648 for hardware one time password calculators.

Dear @ArduinoBot issues fixed - could you be so kind to try again ?


Censoring

Thanks for your effort and for making the implementation available.
I just came across torchsurv and was wondering if it the Weibull  can account for censored data.
Thanks!

Dear @melodiemonod,
Many thanks for your reply. It is working and gives the same results for the NLL as the Tensorflow-Probability implementation in the case of right-censoring.
Any plans to also include left and interval censoring?

Super, thank you for letting us know! We will keep a log of it to demonstrate reproducibility. If you want to share your code below, you are most welcome to.

Any plans to also include left and interval censoring?

You are working with the first release of the package now. We are waiting to get requests from users and then will start addressing them by the most popular in future releases. So possibly in the future if there is interest :)

@melodiemonod Ok thanks!
Please find below the MWE:
###
# Imports
###
import torch
from torchsurv.loss.weibull import neg_log_likelihood
from torch.distributions import Weibull as Weibull_PyTorch

import tensorflow as tf
import tensorflow_probability as tfp
tfd = tfp.distributions
import numpy as np

###
# Data (taken from https://probflow.readthedocs.io/en/stable/examples/time_to_event.html#)
###
np.random.seed(123)
tf.random.set_seed(123)

# Generate time-to-event data
n_samples = 1000
n_obs = 800
n_feat = 2
x = np.random.rand(n_obs, n_feat)
w = np.array([[1.], [-1.]]).astype('float32')
b = np.random.rand(1, 1)
y = tfd.Exponential(tf.nn.softplus(x@w + b)).sample().numpy()

# Generate Weibull Parameters
concentration = np.exp(np.random.rand(n_obs,1))
scale = np.exp(np.random.rand(n_obs,1))

# Simulate purchase times
t_stop = 10 #time of data collection
t1 = t_stop*np.random.rand(n_obs)
t2 = t1 + y[:, 0]
cix = t2>t_stop

# set some observations to censored
# Neg. wait time w/ still no observation
y[cix, 0] = t1[cix]-t_stop

###
# TensorFlow
###
tf.random.set_seed(123)

dist = tfd.Weibull(concentration = concentration, scale = scale)

# Likelihoods of observed time-to-events
obs_ll = dist.log_prob(y)[y>=0]

# Likelihoods of right censored data
right_ll = dist.log_survival_function(-y)[y<0]

# Total NLL
nll_tfp = tf.reduce_sum(obs_ll) + tf.reduce_sum(right_ll)

# Samples
samples_tfp = dist.sample(n_samples)

print(f"NLL: {-nll_tfp.numpy():.4f} \n Sample-Mean: {tf.math.reduce_mean(samples_tfp).numpy():.4f}")

###
# Torchsurv
###
torch.manual_seed(123)

# Log-Params
log_params = torch.tensor(np.concatenate([np.log(scale), np.log(concentration)], axis=1), dtype = torch.float32)

# Time and Event
event_var = torch.tensor(y >= 0).reshape(-1,)
time_var = torch.tensor(y).abs().reshape(-1,)

# NLL
nll_pytorch = neg_log_likelihood(log_params, event=event_var, time=time_var, reduction="sum")

# Initialize Distribution for sampling
weibull_pytorch = Weibull_PyTorch(scale=torch.tensor(scale), concentration=torch.tensor(concentration))

print(f"NLL: {nll_pytorch.numpy():.4f} \nSample-Mean: {weibull_pytorch.sample((n_samples,)).numpy().mean():.4f}")

Thanks @StatMixedML  for the suggestion - I created a backlog issue for future release

Hi @StatMixedML,
Please feel free to check CenTime. In Appendix A, we show how to deal with left and interval-censored data.
I hope this is helpful.
Best,
Ahmed


Regular sync until gossip parent block

resolves #1201

Sync up to current slot and keep it up using onNewSlot
Once we see gossip block parent in our forkChoice, we can stop regular sync

@wemeetagain so I can consistently sync up to current slot but didn't see any gossip blocks in my test (although last week I did see). Do you have any ideas?
I see there are Aggregate_And_Proof gossip message so the forkDigest should be good. I didn't see any BLOCK messages even at LodestarGossipSub so it hasn't touched the gossip validator too.

I'm not sure what could have changed in the past week that could have stopped it :thinking:
If it seems like an issue with gossipsub, you might run the cli prefixed with DEBUG=libp2p:gossipsub  to print gossipsub internal logs.

Today I can receive Gossip block, not sure why it did not work yesterday.

So I can sync to gossip blocks for a while then after a while gossip blocks cannot pass our validator due to incorrect proposer index
const supposedProposerIndex = epochCtx.getBeaconProposer(signedBlock.message.slot);
    if (supposedProposerIndex !== signedBlock.message.proposerIndex) {
      return ExtendedValidatorResult.reject;
    }

Will create a separate issue for it.


[WIP] Implementation of the actual python bindings for DroneCore

This is still a WIP!
Basic concept is using the bindings like this:
from dronecore import Backend, Action

# Connect to a dronecore backend running on the local machine
core = Core(host="<IP_ADDRESS>")

# Initialize the Action plugin
action = Action(core)

# E.g. arm the copter
action.arm().subscribe(on_completed=lambda: print("ARMED!"),
                       on_error=lambda _: print("Could not arm the system!"))

I think I like it :-). Can we merge that in this state already?

I'd actually like to get streaming working properly before - also I have some changes that are not commited yet! Let me check this afternoon, maybe then we can merge!

No worries, it's not urgent :)

It's always urgent! 8). I'd love to move the PX4 CI over to this!

@JonasVautherin FYI
Basic calls and Streams are working just fine, I kept the code pretty consistent so we can build the auto generator ontop of it!
@hamishwillee I don't think the interface will change - I haven't worked with the Swift bindings yet but tried to kept it as close as possible, can you compare and give your OK? :-)

@JonasVautherin I propose we merge and take it as a baseline for the autogenerator - I can't think of anything that has to be changed.


fix: Support nullable for arrays and objects

Describe your changes
This change will allow explicitly setting null to arrays, objects, items of an array of strings, etc.
How best to test these changes
Issue ticket number and link

Codecov Report
Base: 32.25% // Head: 32.30% // Increases project coverage by +0.05% :tada:

Coverage data is based on head (c8e2e28) compared to base (ddf1353).
Patch coverage: 45.23% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #731      +/-   ##
==========================================
+ Coverage   32.25%   32.30%   +0.05%
==========================================
  Files         129      129
  Lines       14392    14420      +28
==========================================
+ Hits         4642     4659      +17
- Misses       9318     9324       +6
- Partials      432      437       +5

Impacted Files
Coverage Δ

schema/reserved.go
100.00% <ø> (ø)

server/services/v1/database/query_runner.go
4.73% <ø> (+0.04%)
:arrow_up:

server/services/v1/database/search_indexer.go
44.95% <0.00%> (-3.09%)
:arrow_down:

schema/collection.go
69.64% <67.85%> (-0.86%)
:arrow_down:

schema/fields.go
77.37% <0.00%> (+0.65%)
:arrow_up:

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

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Add self closing iframe tag

Hi @wakkoism, FYI I've added this change to my "vanilla js" fork over at https://github.com/naton/lity


WASI, Node API, Test Changes

Summary
A smattering of items mainly focused on WASI integration, test updates, and Node API changes.
Components

[X] Closes #440 (with integration tests for dynamic data check)
[X] Closes #495
[X] Closes #493
[X] Closes #494
[X] Closes #484
[X] Closes #498
[X] Fully-basked wit/wasi integration and incorporating wit-deps for shared packages
[X] Allows for the execution of Wasi Wasm components, providing some basics around print, get-current-time, and logging (the latter using the WASI proposal's interface
[X] CID change(s) for Wasm
[X] Remove the need for manually killing/stopping procs in Homestar-runtime integration tests with ChildGuard wrapper util
[X] New basic wasm mods (incorporating host functions and logging)
[X] Parallelize the integration tests 🐕
[X] Health check now validates running DB

nightly lint errors are being fixed in mainline clippy: https://github.com/rust-lang/rust-clippy/issues/12133.

failed tests are the nightlies which should be fixed up soon after the clippy false positive issue.


Sonoff TH10/16 temperature threshold config

A configurable temperature threshold for the heater mode for the Sonoff TH10/16 would be really useful - i.e
I am using a TH16 to trigger a system that heats a hot tub, and it's inefficient to have it cycle rapidly to keep an exact temperature.
I would like it to turn on when it is 2 degrees below the target temperature, and then turn off when it reaches the target.
I am sure this would be useful for other cases where rapid on/off is inefficient, or also where a range of temperatures is acceptable.
Here is how I think it can be implemented:
https://github.com/bwp91/homebridge-ewelink/blob/9ef9c2de83e7fff68960639999cdf487eb7ff15f/lib/device/simulation/th-heater.js#L298-L306
gets replaced with something like (a similar pattern can also be used in th-cooler.js)
if (this.cacheTemp < value - deviceConf.targetTempThreshold) {
    params.mainSwitch = 'on'
    params.switch = 'on'
    newHeat = 'on'
} else if (this.cacheTemp >= value) {
    params.mainSwitch = 'off'
    params.switch = 'off'
    newHeat = 'off'
}

and then to the config https://github.com/bwp91/homebridge-ewelink/blob/9ef9c2de83e7fff68960639999cdf487eb7ff15f/config.schema.json#L1120
add this
"targetTempThreshold": {
  "type": "number",
  "title": "Target Temperature Threshold",
  "description": "You can add a threshold so the device only switches on when the current temperature is at least the threshold away from the target temperature. This can be useful for devices that don't require an exact temperature and you want to reduce the on-off cycles. Must be positive and can include a decimal point.",
  "placeholder": 0,
  "condition": {
    "functionBody": "return (model.thDevices && model.thDevices[arrayIndices] && ['th', 'sc', 'hc', 'panel'].includes(model.thDevices[arrayIndices].deviceModel) && ['heater',  'cooler'].includes(model.thDevices[arrayIndices].showAs) && !model.thDevices[arrayIndices].ignoreDevice);"
  }
}

Thanks! I am testing this now and will report back here in a few days :)

Started testing this and sometimes it does not seem to turn off the TH16 even when the target temperature is reached - today my hot tub got to 55c before I realised 😂, I now think about it.... this was also happening before this targetTempThreshold was added so I think it is a unrelated issue.
I tried to look through the code to help, but I couldn't see anything obvious.
I'm thinking that maybe sendDeviceUpdate is unreliable and the newHeat value might get out of sync so the plugin thinks it does not need to send the device an "off" update??!?...
I think this could be what is happening because if the device is turned off from an external source (e.g. the eWeLink app) nothing is reflected in HomeKit (or the plugin). This might be something useful to be implemented.
on another note this seems odd
https://github.com/bwp91/homebridge-ewelink/blob/3cde4f0ab3487ef33ca55aee2b87ad84f55a3232/lib/device/simulation/th-heater.js#L197
because the the targetHeaterCoolerState is always 0 as defined here
https://github.com/bwp91/homebridge-ewelink/blob/3cde4f0ab3487ef33ca55aee2b87ad84f55a3232/lib/device/simulation/th-heater.js#L134

The code references you have mentioned should be fixed in 8.12.1-beta.1... I will get back to you with explanations about the rest of the points you have mentioned... :)

Ah nice,
I can see the behaviour in that simulating a thermostat (or heater cooler or just a heater) in HomeKit means the thermostat state being on/off does not actually reflect if the switch (heat) is actually on/off... but I was suggesting maybe if a manual switch override occurs - eg the Sonoff device is turned off in app, then the HomeKit thermostat should turn off, and the same the for turning on...
but anyway I think that is a separate pattern from a sendDeviceUpdate "sync".

I'm not saying there is potentially something wrong with these changes I have made for this feature request, but hopefully explaining why the plugin cannot take into account incoming updates from the TH device for heater and cooler simulations

sometimes it does not seem to turn off the TH16 even when the target temperature is reached - today my hot tub got to 55c before I realised

Is it possible that this issue is if there are network issues and an off command fails and the plugin is ignoring updates and using the cache so it thinks the device is off when actually it is on and does not ever try to turn it off again?

Yes, I have a very similar setup and it also works fine for me using ONLY the eWeLink auto mode.
But if I turn that off and use just the home bridge plugin with the "targetTempThreshold" to do the same thing, it works mostly, but then sometimes just does not shut off.
I still think this could be the case

Is it possible that this issue is if there are network issues and an off command fails and the plugin is ignoring updates and using the cache so it thinks the device is off when actually it is on and does not ever try to turn it off again?

Hi,
Closing this just as been a little overwhelmed with issues recently.
If this is still an issue or a feature you would like implemented then please do re-open this ticket!
Thanks for your understanding!


Blocked sites still appear in Google's "Questions & answers" section

Expected Behavior
Blocked sites should be blocked everywhere; I shouldn't see them in Google's "Questions & answers" section.
Actual Behavior
Blocked sites still appear in Google's "Questions & answers" section.
Steps to Reproduce the Problem

Block a site that usually appears in Google's "Questions & answers" section (Quora in the example below)
Find that it's blocked in normal search results but not blocked in the "Questions & answers" section

Specifications

Browser: Microsoft Edge
Other extensions/add-ons:

Search engine: Google
Language: English
Region: Philippines

No problem! :)


Julia 0.3.11 kernel keeps dying

I am experiencing frequent kernel deaths lately. Every time I launch Julia 0.3.11 notebook on juliabox the kernel is unable to start and dies. This happens only occasionally with Julia 0.4.0-rc2 notebooks (but many packages are still not compatible with 0.4 :( ).

Duplicate of #305

@mmagnuski  Could you also report the error IJulia throws? It is usually logged at ~/.juliabox/ijulia_err.log

Contents of ijulia_err.log after kernel death:
[I 18:55:55.318 NotebookApp] Writing notebook server cookie secret to /home/juser/.ipython/profile_default/security/notebook_cookie_secret
[I 18:55:55.318 NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
[W 18:55:55.333 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[W 18:55:55.333 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using authentication. This is highly insecure and not recommended.
[W 18:55:55.334 NotebookApp] Terminals not available (error was No module named terminado)
[I 18:55:55.334 NotebookApp] Serving notebooks from local directory: /home/juser
[I 18:55:55.334 NotebookApp] 0 active kernels
[I 18:55:55.334 NotebookApp] The IPython Notebook is running at: http://[all ip addresses on your system]:8998/
[I 18:55:55.334 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 18:55:55.621 NotebookApp] 302 GET / (<IP_ADDRESS>) 0.66ms
[I 18:55:55.622 NotebookApp] 302 GET / (<IP_ADDRESS>) 0.30ms
[I 18:59:35.228 NotebookApp] Creating new notebook in
[I 18:59:35.230 NotebookApp] Writing notebook-signing key to /home/juser/.ipython/profile_default/security/notebook_secret
[I 18:59:40.185 NotebookApp] Kernel started: 9a57a52d-2b45-459e-b892-860cca62f7b3
[W 18:59:40.193 NotebookApp] 404 GET /kernelspecs/julia-0.3/logo-64x64.png (<IP_ADDRESS>) 6.46ms referer=https://www.juliabox.org/notebooks/Untitled.ipynb?kernel_name=julia-0.3
ERROR: type: instantiate_type: expected TypeConstructor, got Function
 in anonymous at no file:236
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /opt/julia_packages/.julia/v0.3/ZMQ/src/ZMQ.jl, in expression starting on line 234
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/IJulia.jl, in expression starting on line 13
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/kernel.jl, in expression starting on line 4
[I 18:59:43.186 NotebookApp] KernelRestarter: restarting kernel (1/5)
ERROR: type: instantiate_type: expected TypeConstructor, got Function
 in anonymous at no file:236
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /opt/julia_packages/.julia/v0.3/ZMQ/src/ZMQ.jl, in expression starting on line 234
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/IJulia.jl, in expression starting on line 13
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/kernel.jl, in expression starting on line 4
[I 18:59:46.191 NotebookApp] KernelRestarter: restarting kernel (2/5)
ERROR: type: instantiate_type: expected TypeConstructor, got Function
 in anonymous at no file:236
in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /opt/julia_packages/.julia/v0.3/ZMQ/src/ZMQ.jl, in expression starting on line 234
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/IJulia.jl, in expression starting on line 13
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/kernel.jl, in expression starting on line 4
[I 18:59:49.196 NotebookApp] KernelRestarter: restarting kernel (3/5)
[W 18:59:50.924 NotebookApp] Timeout waiting for kernel_info reply from 9a57a52d-2b45-459e-b892-860cca62f7b3
ERROR: type: instantiate_type: expected TypeConstructor, got Function
 in anonymous at no file:236
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /opt/julia_packages/.julia/v0.3/ZMQ/src/ZMQ.jl, in expression starting on line 234
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/IJulia.jl, in expression starting on line 13
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/kernel.jl, in expression starting on line 4
[I 18:59:52.200 NotebookApp] KernelRestarter: restarting kernel (4/5)
WARNING:root:kernel 9a57a52d-2b45-459e-b892-860cca62f7b3 restarted
ERROR: type: instantiate_type: expected TypeConstructor, got Function
 in anonymous at no file:236
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in reload_path at loading.jl:152
 in _require at loading.jl:67
 in require at loading.jl:51
 in include at ./boot.jl:245
 in include_from_node1 at ./loading.jl:128
 in include at ./boot.jl:245
 in include_from_node1 at loading.jl:128
 in process_options at ./client.jl:285
 in _start at ./client.jl:354
while loading /opt/julia_packages/.julia/v0.3/ZMQ/src/ZMQ.jl, in expression starting on line 234
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/IJulia.jl, in expression starting on line 13
while loading /opt/julia_packages/.julia/v0.3/IJulia/src/kernel.jl, in expression starting on line 4
[W 18:59:55.205 NotebookApp] KernelRestarter: restart failed
[W 18:59:55.206 NotebookApp] Kernel 9a57a52d-2b45-459e-b892-860cca62f7b3 died, removing from map.
ERROR:root:kernel 9a57a52d-2b45-459e-b892-860cca62f7b3 restarted failed!
[W 18:59:55.426 NotebookApp] Kernel deleted before session
[W 18:59:55.427 NotebookApp] 410 DELETE /api/sessions/76505f04-c5ec-4c61-a4e1-b5f63ec52e6f (<IP_ADDRESS>) 1.07ms referer=https://www.juliabox.org/notebooks/Untitled.ipynb?kernel_name=julia-0.3

Just as in #305 - removing .julia fixes the problem

Would you please provide the instructions to remove .julia from the JuliaBox?

@RobertoCarlos2 just rm -rf ~/.julia should do it.

Thank you @tanmaykm ! This seems to fix the problem.

removing ~/.julia also works for versions 0.4.2 and 0.5+ which kernels where also kept dying.

this also means we can't install anything anymore, After doing:
shell> rm -rf ~/.julia    # things work!

julia> Pkg.add("Gadfly")    # not anymore

Things break again.


Recent snapshots have broken the resource pack

In the newest snapshots the resource pack doesn't load anymore :c Maybe due to the modifications Mojang brought to shaders ?

Yes that is correct but I already released a changed version that works in the snapshot, you can find it in the other branch here (notice the little feat/mc-1.20.5 in the top left)

Yes that is correct but I already released a changed version that works in the snapshot, you can find it in the other branch here (notice the little feat/mc-1.20.5 in the top left)


no dollar sign showing up in the terminal, hence the terminal is not responding!!!!!!

ADD ISSUE DESCRIPTION HERE
Version: 1.77.3
Commit: 704ed70d4fd1c6bd6342c436f1ede30d1cff4710
User Agent: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/<IP_ADDRESS> Safari/537.36
Embedder: codespaces

### Tasks
- [ ] Add a draft title or issue reference here

### Tasks
- [ ] Add a draft title or issue reference here

`

Details

 `


[WIP] Support of inlining of binop Exprs in overloads

This commit adds support for inlining of binop expressions
in InlineOverload pass. Fix #5064.

@kozlov-alexey thanks for submitting this, I have added it to the review queue.

@kozlov-alexey, the title says "WIP". Are you still working on it?

@sklam Yes, I wanted to add some more changes for solution to work with all operators (not just binops). But it seems my new changes broke some tests (which I didn't notice, since they are skipped on python 3.8). I'll fix that and remove the tag once it's done.

@sklam I finished making changes and tests now pass. Can you please add it to review queue once again?

@sklam, @stuartarchibald Is this really on review? Can you maybe take a look this week an provide initial feedback?

@sklam, @stuartarchibald, Can you please take a look one more time and provide feedback on recent changes? Also do you think we should deal with inlining operator.setitem in scope of this or another PR?

 Also do you think we should deal with inlining operator.setitem in scope of this or another PR?

Would suggest getting this in and handling setitem in a subsequent PR.

14cd412 fixes the 3 typos.

@stuartarchibald I checked 14cd412 and it is fine.

@stuartarchibald I checked 14cd412 and it is fine.

thanks @esc


feat: Add "transaction" pointer on Span

A proposal that we haven't really discussed in details, but was straightforward to implement to showcase. Needed for OTel work (#537).
Problem
Spans know whether they are transactions (e.g. root spans) thanks to isTransaction flag, but there's no nice way to actually "reach" the transaction from a child span. It is needed, for instance, to get a dynamic sampling context for a nested span, in case we want to propagate it to other services.
Proposal
Introduce transaction (name tentative) attribute on Span, that always points to the root span of the local span tree. For actual root spans, transaction is set to nil. With that attribute in place, we can also get rid of isTransaction flag.
Notes and Caveats

A side-effect of removing isTransaction and introducing transaction is that naively created Spans will be transactions by default (since they'll have an empty transaction). We don't really promote or support this usecase anywhere (people should be using StartTransaction and StartSpan), but a thing to keep in mind.
Alternatively, for transaction spans, transaction can store a pointer to itself, and not nil. A small downside is that it will be impossible to create a root level Span instance in one go: it'll be something like t := Span{..}; t.transaction = &t in tests or elsewhere.

Ah, scratch that. Just realized we already have the root span info in spanRecorder. Let me think this over again.


Feature Request: Custom Images

Hey there!
I'd like to ask if it is feasible to add support for custom images? I have a .svg that I'd like to use for my micro.blog's favicon but I wouldn't like the SVG to be the avatar. This plugin is really close to what I'd like to do, but doesn't seem to have support for a custom image.
I believe the image could be uploaded via the assets and then retrieved via URL, right?
Thanks for making this!

Hi, and thanks for checking out my plug-in! 🥰
I've definitely thought about this, but I haven't decided yet whether that feature should be part of this plug-in or a separate one. Micro.blog gives third-party developers like me limited control over settings, and I'm worried Faviconique might become a bit confusing to set up if it tries to do too much. Does that make sense? 😊
I'll definitely think about it, though!
In the meantime, you might have some luck using the Meta tags plug-in as a workaround. You can paste the following snippet there:
<link rel="icon" href="/path/to/your/custom/favicon.svg" sizes="any" type="image/svg+xml">

Got it, that makes a lot of sense. Thanks for the quick reply! 😊


Rework Bread V1

#1

[ ] Rework  Bread v1 into foundry
[ ] Recreate tests in foundry
[ ] Bundle claim rewards and claim yield function (with try catch for claim rewards)
[ ] Add yield claimer role
[ ] Add setYieldClaimer

https://github.com/Astodialo/bread


Bluetooth settings bug

@namkedia,
Thanks for your contribution as a Microsoft full-time employee or intern. You do not need to sign a CLA.
Thanks,
Microsoft Pull Request Bot


Issues with PKS release notes

PKS 1.1.0 section is still there but the release is not available on Pivnet
Minor Typo

VMware NSX-T | 2.1 - Advanced Edition | NST-T versions supported for Pivotal Container Service (PKS)

There is a single component version table for all three version PKS 1.1.0, 1.1.1 and 1.1.2 and the component version still states that the supported Opsmgr version is 2.1.0-2.1.6 which is not the case for publicly available releases as per Pivnet
VMware Harbor Registry version compatible is 1.5.0 whereas there is no 1.5.0 release on Pivnet. I only see three versions publicly available 1.4.2, 1.5.1 and 1.5.2 out of which only 1.5.x is compatible with PKS 1.1.x

Hey @outofmem0ry thanks for this. We've added "Product Snapshots" for each PKS v1.1.x version to clarify component and compatibility information. We've also added a warning box to the PKS v1.1.0 portion of the release notes topic to clarify that PKS v1.1.0 is no longer available from Pivotal Network. Take a look and please raise another issue if you have further feedback. Thanks! https://docs.pivotal.io/runtimes/pks/1-1/release-notes.html


Added "Terms and Conditions" and "Privacy Policy" Pages

Hey @Suchitra-Sahoo,
issue closes #1077
Here's What I Did -

Added a Dedicated "Terms and conditions" Page
Added a Dedicated "Privacy Policy" Page
I tried my best to style the pages to follow the website's theme
Added Navigating Links to the Footer with Hovering Effect.
I Integrated the footer at the bottom and Navbar at the top

Here's are the Results -
https://github.com/Suchitra-Sahoo/AgriLearnNetwork/assets/131389695/e6c51a17-b845-44aa-a476-4396156c3846
Please take a look and review it.
Type of PR

[x] Feature enhancement

Checklist:

[x] I have performed a self-review of my code
[x] I have read and followed the Contribution Guidelines.
[x] I have tested the changes thoroughly before submitting this pull request.
[x] I have provided relevant issue numbers, screenshots, and videos after making the changes.
[x] I have commented my code, particularly in hard-to-understand areas.

@Suchitra-Sahoo PLeaase review it.

Don't add the terms and conditions pages write now. It will be created later.

@Suchitra-Sahoo , So should I remove the "Terms and conditions" Page for now? and keep "Privacy Policy" In this PR.
Later, When there's a need for "Terms and conditions" Page I will send the PR.

Okay let both of them br there just make sure the text is visble clearly so choose some other colour. And make sure after adding privacy policity and terms & condition the footer should be responsive for all screen sizes

@Suchitra-Sahoo Sure, I will do it

@Suchitra-Sahoo Done!.. I've made the Text colors to be readable and Also the Footer is Responsive!
Please Check.

Please update the footer in all the sections.

Also in privacy & terms and condition page the home option of navbar is not working so fix it.

@Suchitra-Sahoo Sure.! Doing it now

Also in privacy & terms and condition page the home option of navbar is not working so fix it.

Oh ok. thanks for clarifying

ok do it then i'll give level2

one more thing the cards are almost toiching the footer so correct it too there should be some space.

Sure @Suchitra-Sahoo , Before that will you revert the merged PR? So that i can Push the updated code to the main branch

ok do it then i'll give level2

Done @Suchitra-Sahoo , Please review the new PR.
Thankyou!


Crossfire rssi in osd

Hi,
I have set up the osd according to this link here:
https://github.com/awolf78/KISS_OSD/wiki
I have followed the instructions the only difference is that I have put it to Aux 4 in the taranis following the link where Oscar describes how to do it for frsky.
When I plug in the kiss fc to the computer I can see the rqly signal in the aux 4 signal so I know its working correctly but it jumps between 1300 and 1995 when off/on. In the osd configurator I put those numbers in and set it to aux 4, but don't get anything other than 0 db in the osd.
Also I've noticed that Arduino says the firmware is very large for the chipset it takes like 98% of it. Any clues as to what is going on here. I purchased this one: https://www.flyduino.net/en_US/shop/product/pr1865-micro-minimosd-kissfc-osd-fw-preflashed-pal-2683?search=Osd
Unfortunately it didn't come with the newest firmware on it and it's been a pain updating it.

I will double check this weekend and finally get it fixed. Thanks for your patience.

Thank you. Is it normal that in Arduino it says there is barely enough space? Is there a way to wipe it clean to free up some space?

That is normal and has nothing to do with the RSSI issue.

With micro minimosd on v2.4RC4.3 I needed it set from 0-1000 but with steele pdb on same firmware it works on -1 and -1. Not sure why but this worked for me.

Steele PDB v2.5 beta OSD.zip
Steele PDB v2.5 beta CONFIG.zip
Try this one. Go in the config tool first and setup min and max RSSI under DISPLAY->RSSI.

Fixed with V2.5 release


Indexing error: piscem index failed to build succesfully ExitStatus(unix_wait_status(132))

Hi,
I was trying to build the spliceu index for the ensembl rat genome.
I used conda to install simpleaf
mamba create -n af -y -c bioconda -c conda-forge simpleaf piscem
Then I downloaded unzipped the rat genome from Ensembl
wget https://ftp.ensembl.org/pub/release-111/fasta/rattus_norvegicus/cdna/Rattus_norvegicus.mRatBN7.2.cdna.all.fa.gz
wget https://ftp.ensembl.org/pub/release-111/gtf/rattus_norvegicus/Rattus_norvegicus.mRatBN7.2.111.gtf.gz
gzip -d Rattus_norvegicus.mRatBN7.2.cdna.all.fa.gz
gzip -d Rattus_norvegicus.mRatBN7.2.111.gtf.gz

Then I ran simpleaf index with these commands
export ALEVIN_FRY_HOME='.'
simpleaf set-paths
ulimit -n 2048

simpleaf index \
--use-piscem \
--output mRatBN7.2.ensembl.v111 \
--fasta Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa \
--gtf Rattus_norvegicus.mRatBN7.2.111.gtf \
--threads 4 \
--ref-type spliced+unspliced

And this is the error I get
2024-03-08T09:11:44.558059Z  INFO simpleaf::simpleaf_commands::indexing: preparing to make reference with roers
2024-03-08T09:11:53.538051Z  INFO grangers::reader::gtf: Finished parsing the input file. Found 5 comments and 1284445 records.
2024-03-08T09:11:55.266274Z  INFO roers: Built the Grangers object for 1284445 records
2024-03-08T09:11:56.059573Z  WARN roers: Found missing gene_id and/or gene_name; Imputing. If both missing, will impute using transcript_id; Otherwise, will impute using the existing one.
2024-03-08T09:11:56.090425Z  INFO roers: Proceed 526642 exon records from 54993 transcripts
2024-03-08T09:12:14.554211Z  INFO roers: Proceed 30562 gene body records
2024-03-08T09:13:31.040646Z  INFO roers: Done!
2024-03-08T09:13:31.067558Z  INFO simpleaf::simpleaf_commands::indexing: piscem build cmd : /home/haberl/mambaforge/envs/af/bin/piscem build -k 31 -m 19 -o mRatBN7.2.ensembl.v111_AAV/index/piscem_idx -s mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa --seed 1 --threads 4
2024-03-08T10:12:52.008871Z ERROR simpleaf::utils::prog_utils: command unsuccessful (signal: 4 (SIGILL) (core dumped)): "/home/haberl/mambaforge/envs/af/bin/piscem" "build" "-k" "31" "-m" "19" "-o" "mRatBN7.2.ensembl.v111_AAV/index/piscem_idx" "-s" "mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa" "--seed" "1" "--threads" "4"
2024-03-08T10:12:52.008910Z ERROR simpleaf::utils::prog_utils: stdout :
====

Constructing the compacted reference de Bruijn graph for k = 31.

Enumerating the vertices of the de Bruijn graph.
31-mer enumeration statistics:
        Number of sequences:    85555.
        Total sequence length:<PHONE_NUMBER>.
        Total number of 31-mers:<PHONE_NUMBER>.
        Number of unique 31-mers:       972718483.
        Number of solid 31-mers:        972718483.
Enumerated the vertex set of the graph. Time taken = 55.9562 seconds.
Number of vertices: 972718483.

Constructing the minimal perfect hash function (MPHF) over the vertex set.
Total number of k-mers in the set (KMC database): 972718483.
Building the MPHF from the k-mer database ./workdir.noindex/piscem_idx_cfish.cf_V.
Using gamma = 10.
Built the MPHF in memory.

Total MPHF size: 1441 MB. Bits per k-mer: 12.4332.
Allocated hash table buckets for the k-mers. Total size: 579 MB.
Total memory usage by the hash table: 2021 MB. Bits per k-mer: 17.4332.
Constructed the minimal perfect hash function for the vertices. Time taken = 85.2591 seconds.

Computing the DFA states.

Opened reference 1 from mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa
Maximum input sequence buffer size used: 4 MB.
Done computing the vertex-states. Time taken = 1337.49 seconds.
Computed the states of the automata. Time taken = 1337.49 seconds.

Extracting the maximal unitigs.
Temporary path file name prefixes: ./workdir.noindex//cuttlefish-path-output-4360066512

Opened reference 1 from mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa
["ref_index_builder", "-i", "mRatBN7.2.ensembl.v111_AAV/index/piscem_idx_cfish", "-k", "31", "-m", "19", "--canonical-parsing", "--build-ec-table", "-o", "mRatBN7.2.ensembl.v111_AAV/index/piscem_idx", "-d", "./workdir.noindex", "-t", "4", "--seed", "1"]
====
2024-03-08T10:12:52.016735Z ERROR simpleaf::utils::prog_utils: stderr :
====
2024-03-08T09:13:31.141014Z  INFO piscem: starting piscem build
2024-03-08T09:13:31.141061Z  INFO piscem: Computing and recording reference signatures...
trimmed polyA tails from 0 records
2024-03-08T09:13:47.407562Z  INFO piscem: done.
2024-03-08T09:13:47.407659Z  INFO piscem: args = ["cdbg_builder", "--seq", "mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa", "-k", "31", "--track-short-seqs", "--poly-N-stretch", "-o", "mRatBN7.2.ensembl.v111_AAV/index/piscem_idx_cfish", "-t", "4", "-f", "3", "-w", "./workdir.noindex"]
****************************************************************************************
Stage 1: 100%
Warning: using counter_max == 1 will cause not storying counters in KMC output file, all counters will be assumed to be 1. This is experimental and is not currently supported in kmc_tools. Will be implemented soon.
Stage 2: 100%

[Building BooPHF]  47.4 %   elapsed:   0 min 39 sec   remaining:   0 min 43 sec
Completed a pass over the k-mer database.
[Building BooPHF]  94.9 %   elapsed:   1 min 21 sec   remaining:   0 min 4  sec
Completed a pass over the k-mer database.
[Building BooPHF]  100  %   elapsed:   1 min 24 sec   remaining:   0 min 0  sec
Closed reference mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa.

Processed 85555 sequences. Total reference length:<PHONE_NUMBER> bases.
Closed reference mRatBN7.2.ensembl.v111_AAV/ref/roers_ref.fa.
====
Error: piscem index failed to build succesfully ExitStatus(unix_wait_status(132))

Could not find anything similar in older issues and would appreciate any hint to where I did a mistake.
Thanks in advance!

Hi @lichtobergo,
Indeed, I think we have to do more work to try to propagate up extra information from the underlying program, error messages like this are hard to debug.  However, exit code 132 is generally an attempt to execute an illegal instruction.  This suggests that, perhaps, the compiled executable contains an instruction not supported on the hardware where the program is being run?  Can you share a little bit of information about the environment (CPU, OS version, etc.) where you are running this?
Thanks!
Rob

Yes. If it works on the other machine, it is evidence of use of an illegal instruction. In that case, maybe we could track it down and determine if it can be / is worth stripping from the conda binary. Alternativel, we could build a binary on the side that doesnt use that instruction (but may be slower). I have some thoughts as to which instructions they might be, if it's indeed the case.
Thanks!
Rob

Dear Rob,
I repeated the exact same commands on my laptop and it finished successfully with the following output
2024-03-11T09:18:28.704504Z  INFO simpleaf::simpleaf_commands::indexing: preparing to make reference with roers
2024-03-11T09:18:31.511848Z  INFO grangers::reader::gtf: Finished parsing the input file. Found 5 comments and 1284445 records.
2024-03-11T09:18:32.178402Z  INFO roers: Built the Grangers object for 1284445 records
2024-03-11T09:18:32.381811Z  WARN roers: Found missing gene_id and/or gene_name; Imputing. If both missing, will impute using transcript_id; Otherwise, will impute using the existing one.
2024-03-11T09:18:32.392738Z  INFO roers: Proceed 526642 exon records from 54993 transcripts
2024-03-11T09:18:36.098701Z  INFO roers: Proceed 30562 gene body records
2024-03-11T09:18:45.641713Z  INFO roers: Done!
2024-03-11T09:18:45.661389Z  INFO simpleaf::simpleaf_commands::indexing: piscem build cmd : /home/light/mambaforge/envs/simpleaf/bin/piscem build -k 31 -m 19 -o mRatBN7.2.ensembl.v111/index/piscem_idx -s mRatBN7.2.ensembl.v111/ref/roers_ref.fa --seed 1 --threads 10
2024-03-11T09:25:13.484207Z  INFO simpleaf::utils::prog_utils: command returned successfully (exit status: 0)

For me that should work. Thank you again! Regarding me this issue can be closed. I don't know if it is worth the effort to track this issue for a soon to be unsupported CPU/architecture.
Kind regards,
Michael

Hi Michael,
Thanks for reporting back! It's hard to say without testing and checking exactly what the offending instruction is, but my guess is that it's probably the bit manipulation instructions, which intel introduced first in the haswell arch, and amd fully supported in the excavator arch. I think we actually have an exposed build flag for that, but turning it off would def hurt performance.  Let us know if you have any further questions!
Best,
Rob

Hi,
I'm posting this here because I encountered the same error (ExitStatus(unix_wait_status(132)) that might be related to a previous issue. I got this error when trying to build an index using the latest human reference from 10x (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz). The command that I'm running looks like this:
ulimit -n 2048
export ALEVIN_FRY_HOME="/home/mkoder/data/alevin_fry_home"
simpleaf set-paths

cd $ALEVIN_FRY_HOME

DATA_DIR="/home/mkoder/data"
REF_DIR="/home/mkoder/reference_genomes/refdata-gex-GRCh38-2024-A"
IDX_DIR="$DATA_DIR/alevin_fry_home/human_2024-A"

simpleaf index \
--output $IDX_DIR \
--fasta $REF_DIR/fasta/genome.fa \
--gtf $REF_DIR/genes/genes.gtf \
--use-piscem \
--rlen 91 \
--threads 6

And this is the exact error message:
And this is the exact error message:Allocated hash table buckets for the k-mers. Total size: 925 MB.
Total memory usage by the hash table: 2814 MB. Bits per k-mer: 15.1983.
Constructed the minimal perfect hash function for the vertices. Time taken = 168.097 seconds.

Computing the DFA states.

Opened reference 1 from /home/mkoder/data/alevin_fry_home/human_2024-A/ref/roers_ref.fa
Maximum input sequence buffer size used: 4 MB.
Done computing the vertex-states. Time taken = 361.109 seconds.
Computed the states of the automata. Time taken = 361.109 seconds.

Extracting the maximal unitigs.
Temporary path file name prefixes: .//cuttlefish-path-output-3615462126

Opened reference 1 from /home/mkoder/data/alevin_fry_home/human_2024-A/ref/roers_ref.fa
["ref_index_builder", "-i", "/home/mkoder/data/alevin_fry_home/human_2024-A/index/piscem_idx_cfish", "-k", "31", "-m", "19", "--canonical-parsing", "--build-ec-table", "-o", "/home/mkoder/data/alevin_fry_home/human_2024-A/index/piscem_idx", "-d", ".", "-t", "6"]

Processed 295650 sequences. Total reference length:<PHONE_NUMBER> bases.
Maximum input sequence buffer size used: 4 MB.
Done writing the compacted graph (in GFA-reduced format). Time taken = 681.216 seconds.
Extracted the maximal unitigs. Time taken = 681.216 seconds.

Maximum temporary disk-usage: 8.9395GB.

Structural information for the de Bruijn graph is written to /home/mkoder/data/alevin_fry_home/human_2024-A/index/piscem_idx_cfish.json.

Constructed the reference compacted de Bruijn graph at /home/mkoder/data/alevin_fry_home/human_2024-A/index/piscem_idx_cfish.
====
2024-07-30T19:52:43.283610Z ERROR simpleaf::utils::prog_utils: stderr :
====
2024-07-30T19:31:08.009639Z  INFO piscem: starting piscem build
2024-07-30T19:31:08.009704Z  INFO piscem: will use . as the work directory for temporary files.
2024-07-30T19:31:08.009715Z  INFO piscem: args = ["cdbg_builder", "--seq", "/home/mkoder/data/alevin_fry_home/human_2024-A/ref/roers_ref.fa", "-k", "31", "--track-short-seqs", "--poly-N-stretch", "-o", "/home/mkoder/data/alevin_fry_home/human_2024-A/index/piscem_idx_cfish", "-t", "6", "-f", "3", "-w", "."]
**********************************************************************************************************************************
Stage 1: 100%
Warning: using counter_max == 1 will cause not storying counters in KMC output file, all counters will be assumed to be 1. This is experimental and is not currently supported in kmc_tools. Will be implemented soon.
Stage 2: 100%

[Building BooPHF]  46.7 %   elapsed:   1 min 17 sec   remaining:   1 min 28 sec
Completed a pass over the k-mer database.
[Building BooPHF]  93.7 %   elapsed:   2 min 36 sec   remaining:   0 min 11 sec
Completed a pass over the k-mer database.
[Building BooPHF]  100  %   elapsed:   2 min 45 sec   remaining:   0 min 0  sec
Closed reference /home/mkoder/data/alevin_fry_home/human_2024-A/ref/roers_ref.fa.

Processed 295650 sequences. Total reference length:<PHONE_NUMBER> bases.
Closed reference /home/mkoder/data/alevin_fry_home/human_2024-A/ref/roers_ref.fa.
directory already exists
====
Error: piscem index failed to build succesfully ExitStatus(unix_wait_status(132))

I'm running Ubuntu 22.04.3 LTS. With the same conda environment, the code finished running successfully on a different system ( Red Hat Enterprise Linux release 8.6 (Ootpa)). It also finishes successfully if I skip the --use-piscem flag.
I would really appreciate your help with this issue. Ideally, I would like to solve this on the Ubuntu system that I'm currently using. If there is any additional information I can provide, please let me know.
Best,
Maruša

Hi @marusakod,
Thanks for posting. Are you using the latest version of piscem? And what version of simpleaf? For a while now, piscem has been the default (i.e. use-piscem has been redundant). I see the above has a message about the directory existing. Can you try writing to a place that doesn't have an index yet (or using the --overwrite flag)?
--Rob

Thanks for the quick response! For the previous run I was using piscem v. 0.6.3 and simpleaf v. 0.15.1. I now tried again with piscem v. 0.10.3 and simpleaf v. 0.17.2 and with the --overwrite flag and I get the exact same error.
Maruša

Thanks,  @marusakod!
One more quick check before digging deeper, can you please run
simpleaf refresh-prog-info
And try once more, and then show the result of
simpleaf inspect
If it’s still not working. In that case maybe I can try in a VM matching your specific OS.
Best,
Rob

Thanks @rob-p ,
I tried again without success. This is the output of simpleaf_inspect:
{
  "builtin_chemistries": [
    "10xv2",
    "10xv2-5p",
    "10xv3",
    "10xv3-5p",
    "10xv4-3p",
    "custom()"
  ],
  "custom_chem_info": "",
  "simpleaf_info": {
    "prog_info": {
      "alevin_fry": {
        "exe_path": "/home/mkoder/miniconda3/envs/simpleaf/bin/alevin-fry",
        "version": "0.10.0"
      },
      "piscem": {
        "exe_path": "/home/mkoder/miniconda3/envs/simpleaf/bin/piscem",
        "version": "0.10.3"
      },
      "salmon": {
        "exe_path": "/home/mkoder/miniconda3/envs/simpleaf/bin/salmon",
        "version": "1.10.3"
      }
    }
  },
  "simpleaf_version": "0.17.2"
}

I don't know if this helps, but I tried also on a slightly updated version of Ubuntu (22.04.4) and I'm getting the same error message as the one posted above, except this time it ends with ExitStatus(unix_wait_status(4))
Best,
Maruša

Hi @marusakod,
Thanks; this is useful.  I was not yet able to reproduce this natively on our server (using the same dependencies installed from bioconda) --- there the index built successfully.  Can you tell me a little bit more about the hardware you're on (e.g. what's the output of cat /proc/cpuinfo)?  The next thing I'll probably try is a VM using your exact OS version to see if I can obtain this behavior.
The perplexing thing to me in your output is the "directory already exists" message. I'm not exactly sure where that is coming from or why it shows up if you try to write the index in a completely new place.
--Rob

Small update:
I put together a docker image with Ubuntu 22.04.4, and installed simpleaf via conda.  Unfortunately (feels strange to say that in this context), the construction succeeded there as well.  I suspect there is either something specific to the hardware on which you're running (in which case the cat /proc/cpuinfo might help suggest differences), or about the filesystem itself.  Out of curiosity, before you attempt to build the index, what is the layout of your $DATA_DIR/alevin_fry_home/?
--Rob

Hi @rob-p ,
before I attempt to build the index, my $DATA_DIR/alevin_fry_home/ is empty. I tried again on a different machine with Ubuntu 22.04.4 and it worked. I attached the outputs of cat /proc/cpuinfo for both systems that I used. The directory already exists message is indeed very strange and I'm not sure which directory this is referring to. I tried using different directories for $ALEVIN_FRY_HOME and for building the index and it's always the same.
not_working_sys_info.txt
working_sys_info.txt
Best,
Maruša

Hi @marusakod,
This is very useful.  Ok; I have a theory.  The non-working system has an AMD Opteron 6376.  This is a 12 year old processor.  I suspect that the compiler flags used in bioconda when building probably emit instructions that cannot be used on this, rather old, CPU.  Overall, we (the devs) should really figure out a policy for "processor" support to determine when a processor is too old to have the necessary capabilities for a tool.
That said, if you really need to run on this machine, the thing to try would be to build a version with the minimal possible instruction set / intrinsics.  I can give that a try if you want (build it in my docker image) and strip out all unnecessary flags.
--Rob

Hi @marusakod,
Ok, here is a binary for piscem (the "offending" program) that is explicitly compiled with all of the fancy instructions stripped away and specifically for the opteron architecture.  However, it's likely to only work on ubuntu 22.04.  Also, because it's not allowed to use BMI2 (bit manipulation instructions), it may be markedly slower than the executable you get from bioconda.  That said, hopefully you can use this if you need to process some samples on this machine.  Please let me know if you give this a try.
Best,
Rob

Hi @marusakod,
Any update here? Have you had a chance to try the custom compiled executable?
—Rob

Hi @rob-p ,
happy to report that the index finished building successfully with the custom executable on Ubuntu 22.04. Thanks a lot!
Best,
Maruša


Update setup.cfg to allow python 3.7+

Update setup.cfg to allow python 3.7+ since MWAA only supports python 3.7

Codecov Report

Merging #12 (4ba9811) into main (8fc7e4c) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main      #12   +/-   ##
=======================================
  Coverage   24.95%   24.95%
=======================================
  Files          14       14
  Lines         501      501
  Branches       55       55
=======================================
  Hits          125      125
  Misses        371      371
  Partials        5        5

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Can't send message when using .net 7 with AOT publish set true

I need your help, I use TelegramBot lib to send message to me, But when I using .net 7 with AOT set true, It allway show error  No parameterless constructor defined for 'Newtonsoft.Json.Serialization.SnakeCaseNamingStrategy'.
This made me can't send msg

This library heavily relies on reflection which is heavily restricted on NativeAOT. We don’t optimize the library for this use case and don’t test.

any repro? your project setup, publish command, target platform.. any useful information would be helpful.

You can try to disable trimming during publish to keep NewtonSoft's code untouched:
https://docs.microsoft.com/en-us/dotnet/core/deploying/trimming/trim-self-contained#publish-with-the-cli
dotnet publish -r win-x64 -p:PublishTrimmed=false

any repro? your project setup, publish command, target platform.. any useful information would be helpful.

only test sample telegrambot for send message function, maybe because AOT make error, I will wait some time, thank you

Can't you replace Json.net in TelegramBot to System.Text.Json in .net core flatform, or anyway to archive this, like asp.net core, I can chose use Json.Net or System.Text.Json

Please follow issue template
If you want to chat, feel free to join our group.

.NET 7 introduced a breaking change in trimming assemblies.

Previous behavior
Previously, only assemblies that were opted-in with <IsTrimmable>true</IsTrimmable> in the library project file were trimmed.
New behavior
Starting in .NET 7, trimming trims all the assemblies in the app by default. Apps that may have previously worked with PublishTrimmed may not work in .NET 7. However, only apps with trim warnings will be affected. If your app has no trim warnings, the change in behavior should not cause any adverse affects, and will likely decrease the app size.

For example, an app that uses Newtonsoft.Json or System.Text.Json without source generation to serialize and deserialize a type in the user project may have functioned before the change, because types in the user project were fully preserved. However, one or more trim warnings (warning codes ILxxxx) would have been present. Now, types in the user project are trimmed, and serialization may fail or produce unexpected results.

If your app did have trim warnings, you may see changes in behavior or exceptions. For example, an app that uses Newtonsoft.Json or System.Text.Json without source generation to serialize and deserialize a type in the user project may have functioned before the change, because types in the user project were fully preserved. However, one or more trim warnings (warning codes ILxxxx) would have been present. Now, types in the user project are trimmed, and serialization may fail or produce unexpected results.

Recommended action
The best resolution is to resolve all the trim warnings in your application. To revert to the previous behavior, set the TrimMode property to partial, which is the pre-.NET 7 behavior.
<TrimMode>partial</TrimMode>

System.Text.Json in reflection mode (which is IMO default) would also suffer from this issue. It should be set up with source generated serialization to be compliant with trimming/AOT scenarios.


Updating Token Metadata

Hi!
Thanks for your work in this library. Do you have support for updating the token metadata for the token metadata program?
If not, can you possibly offer me some directions. I can help with a PR.

released a new version and you can take a look here for update metadata example
https://github.com/portto/solana-go-sdk/blob/main/docs/_examples/program/metaplex/token-metadata/update-metadata/main.go
will support more mpl token metadata program instructions


Laravel Jetstream

Do you know why this dont work with Laravel Jetstream?

Most likely because you're using an older version of Jetstream which used an older version of Inertia.
This Progress library requires 0.6.0 or newer: https://github.com/inertiajs/progress/blob/master/package.json#L28
Hope that helps. 👍