[Installation]: CuPy and Multiprocess raise the AssertionError: daemonic processes are not allowed to have children

Your current environment
PyTorch version: 2.1.2+cu121
Is debug build: False
CUDA used to build PyTorch: 12.1
ROCM used to build PyTorch: N/A

OS: Ubuntu 20.04.6 LTS (x86_64)
GCC version: (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
Clang version: Could not collect
CMake version: Could not collect
Libc version: glibc-2.31

Python version: 3.9.18 (main, Sep 11 2023, 13:41:44)  [GCC 11.2.0] (64-bit runtime)
Python platform: Linux-5.15.0-67-generic-x86_64-with-glibc2.31
Is CUDA available: True
CUDA runtime version: 12.1.105
CUDA_MODULE_LOADING set to: LAZY
GPU models and configuration:
GPU 0: NVIDIA GeForce RTX 4090
GPU 1: NVIDIA GeForce RTX 4090

Nvidia driver version: 535.154.05
cuDNN version: Probably one of the following:
/usr/lib/x86_64-linux-gnu/libcudnn.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_adv_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_adv_train.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_cnn_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_cnn_train.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_ops_infer.so.8.9.0
/usr/lib/x86_64-linux-gnu/libcudnn_ops_train.so.8.9.0
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True

CPU:
Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   46 bits physical, 48 bits virtual
CPU(s):                          96
On-line CPU(s) list:             0-95
Thread(s) per core:              2
Core(s) per socket:              24
Socket(s):                       2
NUMA node(s):                    2
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           85
Model name:                      Intel(R) Xeon(R) Gold 6240R CPU @ 2.40GHz
Stepping:                        7
CPU MHz:                         3128.251
CPU max MHz:                     4000.0000
CPU min MHz:                     1000.0000
BogoMIPS:                        4800.00
Virtualization:                  VT-x
L1d cache:                       1.5 MiB
L1i cache:                       1.5 MiB
L2 cache:                        48 MiB
L3 cache:                        71.5 MiB
NUMA node0 CPU(s):               0-23,48-71
NUMA node1 CPU(s):               24-47,72-95
Vulnerability Itlb multihit:     KVM: Mitigation: VMX disabled
Vulnerability L1tf:              Not affected
Vulnerability Mds:               Not affected
Vulnerability Meltdown:          Not affected
Vulnerability Mmio stale data:   Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Retbleed:          Mitigation; Enhanced IBRS
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB conditional, RSB filling, PBRSB-eIBRS SW sequence
Vulnerability Srbds:             Not affected
Vulnerability Tsx async abort:   Mitigation; TSX disabled
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single intel_ppin ssbd mba ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke avx512_vnni md_clear flush_l1d arch_capabilities

Versions of relevant libraries:
[pip3] mypy-extensions==1.0.0
[pip3] numpy==1.26.4
[pip3] torch==2.1.2+cu121
[pip3] triton==2.1.0
[conda] numpy                     1.26.4                   pypi_0    pypi
[conda] torch                     2.1.2+cu121              pypi_0    pypi
[conda] triton                    2.1.0                    pypi_0    pypiROCM Version: Could not collect
Neuron SDK Version: N/A
vLLM Version: 0.3.3
vLLM Build Flags:
CUDA Archs: Not Set; ROCm: Disabled; Neuron: Disabled
GPU Topology:
GPU0    GPU1    CPU Affinity    NUMA Affinity   GPU NUMA ID
GPU0     X      SYS     0-23,48-71      0               N/A
GPU1    SYS      X      24-47,72-95     1               N/A

Legend:

  X    = Self
  SYS  = Connection traversing PCIe as well as the SMP interconnect between NUMA nodes (e.g., QPI/UPI)
  NODE = Connection traversing PCIe as well as the interconnect between PCIe Host Bridges within a NUMA node
  PHB  = Connection traversing PCIe as well as a PCIe Host Bridge (typically the CPU)
  PXB  = Connection traversing multiple PCIe bridges (without traversing the PCIe Host Bridge)
  PIX  = Connection traversing at most a single PCIe bridge
  NV#  = Connection traversing a bonded set of # NVLinks

How you are installing vllm
Hello, appreciate for the wonderful job.
I've already deploy the vLLM 0.3.0 version with docker (based on the Ray 2.9.3 image and I installed the dependent packages manually) and test my own applications sucessfully.
Now I wanna follow the newest version 0.3.3 of vLLM and get the features which could apply for GPTQ-8bits quantized models.
But when I installed the vllm0.3.3 and required packages, I always got the ERROR from CuPy and multiprocessing with AssertionError: daemonic processes are not allowed to have children.
Anybody meet the same or similar errors? If there is anything that I made it wrong?
The detailed error message is as follows:
2024-03-28 23:34:13 | ERROR | stderr | Traceback (most recent call last):
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
2024-03-28 23:34:13 | ERROR | stderr |     self.run()
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/multiprocessing/process.py", line 108, in run
2024-03-28 23:34:13 | ERROR | stderr |     self._target(*self._args, **self._kwargs)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/llm-controller/server/app/runner.py", line 203, in run_model_worker
2024-03-28 23:34:13 | ERROR | stderr |     app = create_model_worker_app(log_level=log_level, **kwargs)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/llm-controller/server/app/creator.py", line 132, in create_model_worker_app
2024-03-28 23:34:13 | ERROR | stderr |     engine = AsyncLLMEngine.from_engine_args(engine_args)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/async_llm_engine.py", line 628, in from_engine_args
2024-03-28 23:34:13 | ERROR | stderr |     engine = cls(parallel_config.worker_use_ray,
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/async_llm_engine.py", line 321, in __init__
2024-03-28 23:34:13 | ERROR | stderr |     self.engine = self._init_engine(*args, **kwargs)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/async_llm_engine.py", line 369, in _init_engine
2024-03-28 23:34:13 | ERROR | stderr |     return engine_class(*args, **kwargs)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/llm_engine.py", line 126, in __init__
2024-03-28 23:34:13 | ERROR | stderr |     self._init_workers_ray(placement_group)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/llm_engine.py", line 304, in _init_workers_ray
2024-03-28 23:34:13 | ERROR | stderr |     self._run_workers("init_model",
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/engine/llm_engine.py", line 1041, in _run_workers
2024-03-28 23:34:13 | ERROR | stderr |     driver_worker_output = getattr(self.driver_worker,
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/worker/worker.py", line 94, in init_model
2024-03-28 23:34:13 | ERROR | stderr |     init_distributed_environment(self.parallel_config, self.rank,
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/worker/worker.py", line 275, in init_distributed_environment
2024-03-28 23:34:13 | ERROR | stderr |     cupy_utils.init_process_group(
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/vllm/model_executor/parallel_utils/cupy_utils.py", line 90, in init_process_group
2024-03-28 23:34:13 | ERROR | stderr |     _NCCL_BACKEND = NCCLBackendWithBFloat16(world_size, rank, host, port)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/cupyx/distributed/_nccl_comm.py", line 70, in __init__
2024-03-28 23:34:13 | ERROR | stderr |     self._init_with_tcp_store(n_devices, rank, host, port)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/cupyx/distributed/_nccl_comm.py", line 88, in _init_with_tcp_store
2024-03-28 23:34:13 | ERROR | stderr |     self._store.run(host, port)
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/site-packages/cupyx/distributed/_store.py", line 100, in run
2024-03-28 23:34:13 | ERROR | stderr |     p.start()
2024-03-28 23:34:13 | ERROR | stderr |   File "/home/ray/anaconda3/lib/python3.9/multiprocessing/process.py", line 118, in start
2024-03-28 23:34:13 | ERROR | stderr |     assert not _current_process._config.get('daemon'), \
2024-03-28 23:34:13 | ERROR | stderr | AssertionError: daemonic processes are not allowed to have children

Hi, cupy dependency is removed in https://github.com/vllm-project/vllm/pull/3625 recently. You can try to build from source in the latest main branch.

Hi, cupy dependency is removed in #3625 recently. You can try to build from source in the latest main branch.

Thanks for your reply.
I tried it by building from source (branch main) and it worked well w/o cupy dependency.
Thanks again. Looking forward to the formal released version.


Fix uploading Mac results to BQ

The changes from sudo pip install x to pip install x --user python is to get rid of this innocuous warning:
The directory '/Users/kbuilder/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

I tested uploading results to BQ here: https://kokoro.corp.google.com/job/grpc/job/macos/job/pull_request/job/grpc_basictests_opt/1515/ - if you check the commit this is built on, the flags for this job were changed to upload its results to BQ

Issues: #9803 #11179


Investigate options around latency reporting and comparison with server

Is your feature request related to a problem? Please describe.
We are seeing some differences in client request latency and server request latency. This is to investigate ways to track that and find out why.
Describe the solution you'd like
We may want to try two things:

Seeing if we can have the server have a gRPC interceptor that puts a start-to-end duration in gRPC metadata and have a number/percent at which a difference between that and the client duration are large enough to at least trigger a warning
See if there is a gRPC metric that is low-level enough to apply to HTTP2 messages specifically so that we can see if there is a difference between our interceptor-based ones (that surround serialization and other operations) and the low-level ones

It appears that https://pkg.go.dev/google.golang.org/grpc/stats is available to provide lower-level stats, I will confirm how it is implemented in gRPC itself and then look to expose that info.

gRPC stats do happen after interceptors. I have made an example of using gRPC stats at https://github.com/temporalio/samples-go/compare/master...cretz:grpc-stats that require dial options exposed in https://github.com/temporalio/sdk-go/compare/master...cretz:grpc-options.
Will wait for feedback/updates on how to proceed.


JS file can't be found  in chrome devtools sources when using @component  templateUrl

By now,I still can't find a way using *.ts to debug my ionic2 code!
I find  a temporary solution to debug the  js .
project ' ionic-commerce-app'
When using 'ionic build' command ,all src files are compiled and copy to .tmp directory,

But I found strange thing !
If using sytax @component {templateUrl:'about.html'},we can't find the file in chrome developer tools sources.the code can't be set breakpoint to debug.

when I replace the 'templateUrl' to 'template' ,the file can be found in chrome dev sources . and can be set breakpoint to debug.

Can't  I using templateUrl in code.If using templateUrl how to debug it.

Would you be able to update to the latest version? The dev builds no longer use the .tmp directory.

thanks ,I use the latest 0.0.29 ,but it doesn't generate all files

Hello @six006 , thanks for testing! I am going to close this issue as a duplicate of #101 . Thanks!


fix zsh node version autochange not installing node version

@PeterDaveHello (from #1306) - can you confirm that this is the correct fix?

I'll test it :+1:

I think putting nvm use in the else condition of the above if would be better since nvm install will also change the version, we don't need to do it twice, right?

yep that makes more sense

so is this good?


Email OTP and TOTP as the first authentication step in MFA

Describe the issue:
When configuring the email OTP or TOTP as the first step of the MFA flow, the following error will appear.
[2022-08-09 17:29:44,662] [c6e227d4-7fe9-4aa4-90ae-2dd7f5dd9049] ERROR {org.wso2.carbon.identity.application.authentication.framework.handler.step.impl.DefaultStepHandler} - Authentication failed exception! Can not find the authenticated user

How to reproduce:

Configure and OIDC sample app using management console.
Configure MFA using one or more steps and add email otp and totp as authetication options for the first step
Log into the sample app
Select Email OTP as the authetication method.
Login error pops as displayed in the above image

Expected behavior:
Email OTP and TOTP should not be able to allow to use as the first step of MFA
Environment information (Please complete the following information; remove  any unnecessary fields) :

Product Version: IS 6.0.0 RC1
OS: macOS 12.5
Database: MySQL
Userstore: JDBC

Optional Fields
Related issues:

Suggested labels:

Same issue exists for SMS OTP

This issue is being closed due to extended inactivity. Please feel free to reopen it if further attention is needed. Thank you for helping us keep the issue list relevant and focused!


[WIP] Implement base ScriptVisitor

Fixes #186
Marked as WIP because you'll probably have comments on the design.

Hi @xoofx,
I changed the implementation to use double dispatch, as in the "canonical" visitor pattern. It still has two differences with the canonical pattern:

The Visit methods return a ScriptNode, rather than void. This makes it easier to make a visitor that rewrites the AST.
I kept the "context" bit, because it has been very useful to me. If you don't like it, I can drop it; if I make the VisitCore method virtual, it can be easily added by a derived implementation.

ScriptNode would also provide a common abstract method for getting the number of child nodes and GetChildrenAt for example. Then a default visitor can use that to iterate on the nodes and call their Accept method. Then a default visitor can use that to iterate on the nodes and call their Accept method.
GetChildrenAt would have to be implemented by each ScriptNode subclass (it is similar to Roslyn design).

Somehow I missed that bit... I'll see if I can add this. It sure would make the whole thing simpler.

OK, in fact it's going to be difficult to implement a DefaultVisit: because of the ability to rewrite the AST, the visitor needs to be able to recreate a node with different children. So I can't just work with abstract children, I need to know which children they are.
Of course, I could drop the whole AST rewriting capability, but it would make the feature less useful to me.

Somehow I missed that bit... I'll see if I can add this. It sure would make the whole thing simpler.

Yeah, it is usually easier to work like this, as it put the implementation detail in the class. But this visitor doesn't return new node.

OK, in fact it's going to be difficult to implement a DefaultVisit: because of the ability to rewrite the AST, the visitor needs to be able to recreate a node with different children. So I can't just work with abstract children, I need to know which children they are

So you can't reuse the same implementation than the visit above. For example, Roslyn is generating these rewriter
[https://github.com/dotnet/roslyn/blob/8017891b5b8174526ba43a8bb46638c2a8618626/src/Compilers/CSharp/Portable/Generated/Syntax.xml.Main.Generated.cs#L1310-L1956] which inherits CSharpSyntaxVisitor<TResult>.
While for CSharpSyntaxVisitor.DefaultVisit it is following here the general method.
So you would have to write similar code to what you wrote in the Visitor. Just that it is a particular visitor replacing node, node just visiting or even creating new type of results (e.g not nodes).
It's ok to have a ScriptVisitor, a ScriptVisitor<TResult> and a ScriptRewriter (which would be your actual ScriptVisitor)

I'm not sure I understand... What would you like me to do exactly? Write separate visitor and rewriter classes?

I'm not sure I understand... What would you like me to do exactly? Write separate visitor and rewriter classes?

Yeah, they can't be written in the same class, it's very similar to Roslyn. You will have 3 classes:

ScriptVisitor which can use a DefaultVisi() implementation that would rely on  ScriptNode.GetChildrenCount / ScriptNode.GetChildrenAt from ScriptNode
ScriptVisitor<TResult>  which would have a DefaultVisit empty
ScriptRewriter inheriting from ScriptVisitor<ScriptNode> which is actually similar to what you have written, implementing the Visit methods.

It's not very far from what you have. Though, the additional work is to provide ScriptNode.GetChildrenCount/ScriptNode.GetChildrenAt and their derived implementations for each ScriptNode implem.

Ah, I see.
Not sure I see the point of ScriptVisitor<TResult>, though... The default implementation is useless, and if you ever want to make an implementation than returns anything other than ScriptNode, you need to redo all the work of walking the child nodes. Do you have a specific use case in mind?

BTW, is there a particular reason to expose ChildrenCount/GetChildrenAt rather than just a IEnumerable<ScriptNode> Children property? It would be (slightly) less painful to implement. Is this for performance reasons?

Not sure I see the point of ScriptVisitor, though... The default implementation is useless, and if you ever want to make an implementation than returns anything other than ScriptNode, you need to redo all the work of walking the child nodes. Do you have a specific use case in mind?

No personal use case right now for ScriptVisitor<TResult>, it's ok not to introduce it as it would not break the API.

BTW, is there a particular reason to expose ChildrenCount/GetChildrenAt rather than just a IEnumerable Children property? It would be (slightly) less painful to implement. Is this for performance reasons?

Yeah, but that's ok to expose only a Children property for now and use yield. We can add ChildrenCount/GetChildrenAt later if necessary

I eventually implemented the ScriptVisitor<TResult>, because it impacts the signature of the ScriptNode.Accept method, so it would have been a bit messy to add it later. And this way there's not need for an Accept(ScriptRewriter) method.
I renamed the existing tests to ScriptRewriterTests, but I didn't add tests for the new ScriptVisitor yet. I can't think of a good approach to test it. Any idea?

I'm gonna probably pull your PR into the new branch devel-3.0 as I going to need a rewriter in that branch, and as it is a new version allowing breaking change API, I will see if there is anything that I could improve with your work. Thanks a lot!

Closing this branch as your PR is merged into devel-3.0. If you want to iterate on it, feel free to open a PR on this branch.

I'm gonna probably pull your PR into the new branch devel-3.0 as I going to need a rewriter in that branch, and as it is a new version allowing breaking change API, I will see if there is anything that I could improve with your work. Thanks a lot!

Fine by me, thanks!


supporting private keys other than RSA

It is enough to use OpenSSL::PKey.read to handle private keys.
In the case of key or passphrase is invalid, the exception class and the message are changed.
Is this acceptable? Anyway, we should not use File.open without #close (or block) too read a key.

I found that each failing check is caused by the following change:
https://github.com/ruby/openssl/commit/6c09fd3ef5422d798f6674094b9f222c3abae660
The simple way to pass a spec is to not specify an exception class.
By the way, is there any plan to drop supporing old versions of ruby?
As you may know, even 2.7 is in security maintainance phase, 2.6 and previous versions have reached an EOL.

By the way, is there any plan to drop supporing old versions of ruby? As you may know, even 2.7 is in security maintainance phase, 2.6 and previous versions have reached an EOL.

Yes, plan is to drop support for some older versions of ruby.
However there are Long Term Support OSes that have old versions of ruby in them (Ubuntu LTS,  Red Hat Enterprise Linux). For examples Ubuntu 18 LTS - Bionic Beaver has ruby 2.5.1). And Ubuntu 14 Trusty Tahr doesn't reach EOL until April 2024.
Need to work out which to support in the next release.

Just checked and Redhat Enterprise Linux 7 comes with Ruby version <IP_ADDRESS>8-39.el7_9.
Amazingly RHEL7 has maintenance support until 30 June 2024 and Extended
Lifecycle Support until 30 June 2026.

Thanks for your informations! I omitted the exception class on the spec.

Would it be possible to add an example key into /spec/fixtures, so that it is possible to test that this works?

I'm sorry, I'm late. I prepared the EC keys with and without password encrypted, and added the specs for those EC keys (almostly copied from the specs for RSA keys :).

Thank you very much for updating this PR to include some tests.
Sorry to not merge it for so long.


Small fix of UserController

Related to issue #3

Spree:
This plugin doesn't work out of the box without this fix. Why isn't there a test that catches this? How did this code get live?

I can't reproduce this issue on 0-70-stable branch or master (which is not 1.0.0.rc2).
Please refile if its' still happening for the relevant branch, with detailed steps on how to reproduce.


add support for fullscreenchange event to WidthProvider ?

App doesn't auto-resize when I changed the browser to fullscreen mode. It also doesn't resize when I switch the browser back to the normal mode. So it would be nice if the WidthProvider also listens to window's "fullscreenchange" event. I don't know if this is the intention of the library or not. I hope I didn't ask for too many things.

Yes, this is why I suggest to simply write your own if you need more
functionality. Watching the window's width and dealing with browser quirks
is not the domain of this module.
On Oct 16, 2016 3:53 PM, "Thanh Ngo"<EMAIL_ADDRESS>wrote:

App doesn't auto-resize when I changed the browser to fullscreen mode. It
also doesn't resize when I switch the browser back to the normal mode. So
it would be nice if the WidthProvider also listens to window's
"fullscreenchange" event. I don't know if this is the intention of the
library or not. I hope I didn't ask for too many things.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
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.

Oh. Okay, thank you very much! Now I see the WidthProvider becomes my real business now.


End to end test for Kibana liveness

This makes sure we get a response the Kibana viewer UI as well as checking for the Kibana logging service and pod health. Addresses part of #10550
@quinton-hoole @a-robinson

nits, but otherwise LGTM. Please open an issue to speed up the failure case as per comments.
can-be-merged once Jenkins e2e passes (Shippable won't add any more usful signal, so it can be ignored if it flakes).

Issue for speeding up failure case no longer nee3ded, as per in-person discussion and code review comment.  There is only one pod, despite the apparent loop.

LGTM, ok-to-merge

LGTM, ok-to-merge

@k8s-bot test this please

@k8s-bot test this please

@vmarmol this can be merged now.  All tests passed, and code is LGTM.


add endpoint routing

Changes based on this GitHub comment and the sentence just above URL matching

@stevejgordon  @andrewlock @channon @dotnetshadow @joshua-mng


Deploy to GitHub packages

See
publishing workflow: https://github.com/ioki-mobility/SentryProguardGradlePlugin/blob/f83d2a95372c40a87aac6c804b648f8e7a9f4bb8/.github/workflows/publish-to-gpr.yml
code for publishing:
https://github.com/ioki-mobility/SentryProguardGradlePlugin/blob/f83d2a95372c40a87aac6c804b648f8e7a9f4bb8/build.gradle.kts#L32-L76

This is now on maven central.
No need for GitHub packages anymore..


Jump-to-cursor behaviour glitches horizontal scrollbar & text rendering

Prerequisites

[x] Put an X between the brackets on this line if you have done all of the following:

Reproduced the problem in Safe Mode: http://flight-manual.atom.io/hacking-atom/sections/debugging/#using-safe-mode
Followed all applicable steps in the debugging guide: http://flight-manual.atom.io/hacking-atom/sections/debugging/
Checked the FAQs on the message board for common solutions: https://discuss.atom.io/c/faq
Checked that your issue isn't already filed: https://github.com/issues?utf8=✓&q=is%3Aissue+user%3Aatom
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Description
For a file with enough lines to require vertical scrolling, placing the cursor at the bottom and scrolling to the top will put the cursor out of the view. Pressing a key (eg. spacebar) will cause the view to jump down to the cursor (expected behaviour), but in the process glitches the horizontal scrollbar (if present) into appearing further up the window than it should. The text beneath the scrollbar will also disappear in chunks, likely because it is no longer considered "visible". In the extreme case, no text will be rendered at all and the view will appear devoid of text (like a blank file).
Swapping to a different tab/application and back resolves the issue. Trying to scroll horizontally manually also fixes the issue. Closing the find/replace box fixes it.
Steps to Reproduce

Run atom --safe
Type random gibberish for many lines, at least until vertical scrolling is required
Place cursor on bottom line
Scroll to top, such that cursor is below view window
Press spacebar
Observe that horizontal scrollbar has moved, and text will disappear while still in view.

Expected behavior: [What you expect to happen]
It jumps to cursor and behaves as if the user scrolled there like normal.
Actual behavior: [What actually happens]
Glitches the horizontal scrollbar up the view window and causes text to derender early.
Shown in following GIF (horizontal scrollbar not present, but text rendering glitch shown)

Reproduces how often: [What percentage of the time does it reproduce?]
100%
Versions
apm  1.18.8
npm  3.10.10
node 6.9.5 x64
python 2.7.10
git 2.13.6
Atom    : 1.22.1
Electron: 1.6.15
Chrome  : 56.0.2924.87
Node    : 7.4.0
macOS 10.13.1

@Aerijo thanks for reporting.  This should already be fixed in the Atom 1.23 betas.


Add sample for write

Was using this README to do Cosmos DB data migration with Azure Databricks and realized the sample code for write was missing. I think adding this would greatly help anyone learning to use Databricks for Cosmos DB data migration!
Description
Please add an informative description that covers that changes made by the pull request and link all relevant issues.
If an SDK is being regenerated based on a new swagger spec, a link to the pull request containing these swagger spec changes has been included above.
All SDK Contribution checklist:

[ ] The pull request does not introduce [breaking changes]
[ ] CHANGELOG is updated for new features, bug fixes or other significant changes.
[ ] I have read the contribution guidelines.

General Guidelines and Best Practices

[ ] Title of the pull request is clear and informative.
[ ] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For more information on cleaning up the commits in your PR, see this page.

Testing Guidelines

[ ] Pull request includes test coverage for the included changes.

Thanks for the prompt review @kushagraThapar ! @FabianMeiswinkel Please let me know if any changes are needed.

Hi @kushagraThapar , could you please take a look at this PR? Thanks!

@xinlian12  / @FabianMeiswinkel  - please take a look at this.

Hi @xinlian12, could you please have a look at this PR? Thanks!


Change production database provider to SqLite

The database configuration was set to SqlServer by mistake

Merged without review, due to minor change in configuration. No Change in structure or functionality.


Open alert in the app (2.0.0-alpha.52)

The api changed from using the popup (overlay) to  nav.present(alert). I have however since then the problem of that can open popups only in pages. I'm trying to open a popup in the app.js but couldn't since the nav controller is not available yet. Any idea how to overcome this?

Do you have an ion-nav in your app? I'm not sure what you mean by "since the nav controller is not available yet".
Here are some examples:
https://github.com/driftyco/ionic/blob/2.0/ionic/components/alert/test/basic/index.ts#L17

Assumed goal: run navControllerInstance.present() and other NavController methods from within the @App()-decorated class
Out of habit, I would try something like this:
ionic start --v2 --template blank navtest
...
diff --git a/app/app.js b/app/app.js
index 5ffbd11..68d6db6 100644
--- a/app/app.js
+++ b/app/app.js
@@ -1,4 +1,4 @@
-import {App, Platform} from 'ionic/ionic';
+import {App, Platform, NavController} from 'ionic/ionic';
 import {HomePage} from './pages/home/home';

@@ -7,7 +7,7 @@ import {HomePage} from './pages/home/home';
   config: {} // http://ionicframework.com/docs/v2/api/config/Config/
 })
 export class MyApp {
-  constructor(platform: Platform) {
+  constructor(platform: Platform, nav: NavController) {
     this.rootPage = HomePage;

     platform.ready().then(() => {

That produces EXCEPTION: No provider for NavController! (MyApp -> NavController) in the browser... possibly the same problem@afrad had?
That injection approach works fine within a @Page()-decorated class - perhaps because its directive always happens to be a child of <ion-nav> in practice, whereas the @App()-class is a parent of <ion-nav>?:
@App({
  template: '<ion-nav [root]="rootPage"></ion-nav>',

Given that realization, I would ask "how do I get a reference to a child component's class in Angular 2"?
http://stackoverflow.com/a/34517518
https://angular.io/docs/ts/latest/api/core/ViewChild-var.html
https://angular.io/docs/ts/latest/api/core/QueryMetadata-class.html
Evaluation of the @ViewChild()-approach within the --template blank app:
diff --git a/app/app.js b/app/app.js
index 5ffbd11..f04f4ec 100644
--- a/app/app.js
+++ b/app/app.js
@@ -1,12 +1,15 @@
-import {App, Platform} from 'ionic/ionic';
+import {AfterViewInit, ViewChild} from 'angular2/core';
+import {App, Platform, NavController, Alert} from 'ionic/ionic';
 import {HomePage} from './pages/home/home';

 @App({
-  template: '<ion-nav [root]="rootPage"></ion-nav>',
+  template: '<ion-nav #navctl [root]="rootPage"></ion-nav>',
   config: {} // http://ionicframework.com/docs/v2/api/config/Config/
 })
-export class MyApp {
+export class MyApp implements AfterViewInit {
+  @ViewChild('navctl') nav:NavController;
+
   constructor(platform: Platform) {
     this.rootPage = HomePage;

@@ -27,4 +30,16 @@ export class MyApp {
       // StatusBar.setStyle(StatusBar.LIGHT_CONTENT)
     });
   }
+
+  ngAfterViewInit() {
+    console.log('nav is', this.nav);
+
+    let alert = Alert.create({
+      title: "New Friend!",
+      body: "Obi wan Kenobi just accepted your friend request!",
+      buttons: ['Ok']
+    });
+
+    this.nav.present(alert)
+  }
 }

This approach does seem to get the desired NavController reference; from Safari's console:
nav is – Nav {elementRef: ElementRef_, _id: "i0", parent: null, …}
And it does produce an alert when the app starts. But it also seems to block
the root page from loading: The root page does not show up behind the alert,
nor does it appear when the alert is dismissed.
(Ionic 2.0.0-alpha.54)

Replacing this.nav.present(alert) in ngAfterViewInit() with setTimeout(() => this.nav.present(alert), 1000) seems to allow the root page to load and function as expected.

@tomsun This will work only if the loading is faster than 1 second.

( @afrad sure, not a robust solution, not really a solution at all, just an observation for debugging purposes :-) )

A possible workarround is to use an own page for the popup. I don't like it. I miss here the good old $ionicPopup.

To solve this issue I would recommend putting the alert within your root page, and not in the startup script of your app.


composer's hash changed

Using docker-compose and
ERROR: Service 'php-fpm' failed to build : The command '/bin/sh -c php -r "copy('https://getcomposer.org/installer', 'composer-setup.php');"     && php -r "if (hash_file('sha384', 'composer-setup.php') === '795f976fe0ebd8b75f26a6dd68f78fd3453ce79f32ecb33e7fd087d39bfeb978342fb73ac986cd4f54edd0dc902601dc') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;"     && php composer-setup.php --filename=composer     && php -r "unlink('composer-setup.php');"     && mv composer /usr/local/bin/composer' returned a non-zero code: 1
I downloaded the https://getcomposer.org/installer file and the sha384 hash is now
c31c1e292ad7be5f49291169c0ac8f683499edddcfd4e42232982d0fd193004208a58ff6f353fde0012d35fdd72bc394

https://github.com/Volmarg/personal-management-system/commit/79609ab83aa5120a3dd0c28da3cb255c0e76af49
Fixed it and got it going on my system.

Hey there,
Will take a look on this at weekend as I will be releasing new version with Symfony5 support.

This will have to wait a bit as i want to update the new documentation up to the point where it at least equals the old one with content before i make the S5 release.

Sadly I'm unable to test that as I've pretty much like 1mb limited connection and this isn't going to change anytime soon. Could You maybe retest it and let me know if this is still up to date? I will just make the change in my repository since I'm unable to handle that.

Hey, I had same issue and I can confirm that this pull fixes issue regarding composer-setup.php hash

@ThellraAK Thanks for providing the fix, since there was no pull request, I've just copied it.
@insajd Thanks for info
I've updated the main with the hash.


exampleSite content references non existent tweet

Hello @bjacquemet
I am one of the maintainers of Hugo Themes.
There is a reference to a non existent tweet in the content files of your theme's exampleSite.
ERROR 2020/01/03 17:25:32 Failed to get JSON resource "https://api.twitter.com/1/statuses/oembed.json?hide_thread=1&id=%!s(int=1120412132036706305)&dnt=true": Failed to retrieve remote file: Bad Request

This results in a broken demo on the Hugo Themes website.
I tried to make your theme inherit its content from the hugoBasicExample repo, so that the demo generates.
However this resulted in an empty homepage since your theme has a custom portfolio section and even though you are using Hugo's internal mainSections you have hardcoded the section whose content is displayed on the index page.
To fix the demo you need to remove the reference to the non-existent tweet.
Also note that as stated in the Hugo Themes README:

Theme Maintenance

It is of paramount importance that a Hugo theme's demo generates with the latest version of Hugo.

Theme authors need to keep an eye on future Hugo releases and provide patches as needed.

The Hugo Themes Showcase always uses the latest Hugo version to generate its website.

If a theme demo breaks and remains so for more than 30 calendar days, we may remove it from this repository without further notification.

Hi @onedrawingperday
thanks very much for the heads up.
I wonder why it is resulting in an error on your side. Here is the page containing the tweet deployed with Netlify: https://personal-web-example.netlify.com/post/shortcodes/#add-a-single-tweet
The tweet is showing - I deliberately chose an account and tweet that wouldn't be removed

@bjacquemet
Right. So this ERROR is due to recent Hugo updates.
The external demo is generated with "Hugo 0.54.0" but the Hugo website generates always with the latest Hugo.
Your theme's demo has been broken since last October.
Hugo 0.59.0 introduced support for typed bool, int and float in shortcode params. Also see: https://github.com/gohugoio/hugo/pull/6376
Upon closer inspection the request generated by the tweet shortcode that is used in your theme points to a non-existent URL:
https://api.twitter.com/1/statuses/oembed.json?hide_thread=1&id=%!s(int=1120412132036706305)&dnt=true"

This part in particular:
- %!s(int=1120412132036706305) -

The tweet ID is outputted as an int due to the way that the tweet-single parameter is entered  ie.{{< tweet-single<PHONE_NUMBER>036706305 >}}
To fix the ERROR you will need to either change the shortcode input so that the tweet ID is a string by wrapping it in quotes like so: {{< tweet-single "1120412132036706305" >}}
OR
I think it is preferable to do this directly within the shortcode by changing [line 6])(https://github.com/bjacquemet/personal-web/blob/master/layouts/shortcodes/tweet-single.html#L6) of tweet-single.html to something like the following:
{{- $tweetID := print (index .Params 0) -}}
{{- $url := printf "https://api.twitter.com/1/statuses/oembed.json?hide_thread=1&id=%s&dnt=%t" $tweetID $pc.EnableDNT -}}

Once you issue a fix feel free to close this issue.

Thanks a lot. Fixed in the last commit


Added Fragment to Reads

This pull-request implements the Fragment representation for Reads, which is mentioned in more detail in https://github.com/ga4gh/schemas/issues/212.

This seems okay to me, being pedantic, maybe change the comment:
"Each fragment represents a single stretch of a DNA molecule. This enables
+fragment reconstruction of reads which belong to the same fragment."
to
"A fragment represents a contiguous stretch of a DNA or RNA molecule. Reads can
be associated with a fragment to specify they derive from the same molecule."

Good point.  While we are likely to do a documentation pass on the schemas as a whole at some future time it certainly doesn't help to get this in shape from the start.

I like precision as well.  Sean, after updating locally do I just push it again?  I haven't done an update to a PR after pushing pull-request before.
Thanks,
Paul

Once you commit locally and push to GitHub it should update the pull request.

Amazing!
Many thanks Sean and Benedict,
Paul

+1, @saupchurch I assume you're 1+ too?

I was expecting the more hierarchical approach described in #212:
record Fragment {

  /* The fragment ID. */
  string id;

  /* The ID of the read group this fragment belongs to. */
  string readGroupId;

  /* The collection of ReadAlignment which belong to the same fragment. */
  array<ReadAlignment> readAlignments = [];

}

Just wondering what drove the change.

It seemed a lighter touch to me to pull the reads in a fragment by searching on the fragmentId in reads rather than have an object array in Fragment.  Both approaches are acceptable to me; I guess it depends on how we want to query interface to look.

@fnothaft Do you have strong feelings towards the hierarchical approach or are we good to merge?

I am OK with merging; we can always modify later.

+1 looks good to me.

Thank you :)

Hi all -- apologies for chiming in a bit late, but I have both process and substance concerns on this PR.
Re process:

I don't know if all the stakeholders have paid attention. When we stopped the regular Reads Task Team meetings, we discussed the risk of PRs not getting noticed, and I think we agreed on some sort of louder "call for closure", with appropriate waiting period, to compensate for the lack of meetings. In particular, I'd want to be sure that server implementors have had a chance to weigh in, since changes to an existing spec make work for them. I don't remember if we agreed on specifics, though -- @skeenan, do you remember more details?

Re substance:

I don't understand how this change would be used as is. It looks like it defines a new Fragment datatype consisting of nothing but an id, and then adds a fragmentId to the ReadAlignment, next to the existing fragmentName field. Without any methods changes, how does that help application developers?
If we were to add a new method that uses fragmentId (e.g. "a method to query all the reads for a fragment", as discussed in #212), how would that be any better than just adding a method that searches by fragmentName instead?
Adding such a method is potentially expensive, since it likely requires server builders to maintain an index of all ReadAlignments by fragmentName. That might be worth it, but I'd want to hear from application developers to understand how much work it saves them, and hear from server builders on how much work it costs them, and make sure the tradeoff makes sense.

@dglazer I can't comment on substance save to note that the PR has received more than 4 weeks of discussion and 3 +1s

-- @skeenan, do you remember more details?

the minutes  of 28th January DWG call record, amongst other things, that we agreed discussions on Reads API modifications would be conducted via GitHub Issues/PRs and voting. We also trailed and discussed this PR on our 25th March DWG call

Hi @dglazer some comments below
Re process:

- I don't know if all the stakeholders have paid attention. When we stopped the regular Reads Task Team meetings, we discussed the risk of PRs not getting noticed, and I think we agreed on some sort of louder "call for closure", with appropriate waiting period, to compensate for the lack of meetings. In particular, I'd want to be sure that server implementors have had a chance to weigh in, since changes to an existing spec make work for them. I don't remember if we agreed on specifics, though -- @skeenan, do you remember more details?

I've been tasked with looking through the issues on a biweekly basis to see if there are issues or PRs that would have effected the ReadTaskTeam, if this were still an active working group. Those issues are to be tagged with the ReadTaskTeam label and discussion is solicited via the issue, or bringing to the attention of the larger DWG committee during those meetings.

- I don't understand how this change would be used as is. It looks like it defines a new Fragment datatype consisting of nothing but an id, and then adds a fragmentId to the ReadAlignment, next to the existing fragmentName field. Without any methods changes, how does that help application developers?

The motivation comes from the way the RNA-Seq community works with read data, and how that differs from DNA. fragmentName is problematics, since a lot of tools change QNAME, and hence fragmentName, to add information at the end to signify which paired end this read represents. In FASTQ, the QNAME are equal, but the reads are in separate files, with filename representing the read direction. A naive FQ -> SAM translation would lose that information.
- If we were to add a new method that uses fragmentId (e.g. "a method to query all the reads for a fragment", as discussed in #212), how would that be any better than just adding a method that searches by fragmentName instead?

See above, but essentially it would have to be a prefix-matching index. Possible, but not ideal, and who knows what other changes to QNAME happen out there. fragmentID makes the semantics much clearer when translating from other formats. Up for discussion is whether we also want orientation information preserved.

@skeenan , @delagoya -- thanks for responding. (And @delagoya, thanks for your ongoing issue curation.)
Re process -- sorry I missed the March 25 DWG meeting (I was talking at a conference); I'll read meeting minutes more closely in the future. I was following the PR itself, but since it only had a single +1 up until two days ago, I didn't treat it as urgently as I should have.
Re substance:

so you're saying that fragmentName (aka QNAME) is not unique in the real world? I had missed that point in the discussion about this issue, and comments in the schema. Unfortunate, and feels broken to me (why even bother having, and storing, a fragment name if one fragment can have two names?), but if we have to live with it, let's at least document it.
I'm curious -- what tools mess with QNAME, and is there a good reason for doing so? (Given that SAM already has flags that indicate which paired end the read comes from, that we've captured using the readNumber field.)
even if we can't use fragmentName, I don't think adding a fragmentId adds any value unless we also define and implement new methods. If I'm missing something (certainly possible), please explain. If not, I suggest we revert the 'new noun' until we also agree on the 'new verb' that makes it useful.

When a read pair has multiple mappings, it is insufficient to keep track of all the fragment alignments just by QNAME. There are several ways to add the information. How are star/tophat/etc dealing with this issue? It is important to make sure the feature in the schema used in practice.

Tophat seems to have an interesting approach as I quickly looked through the code.  It might be good if someone else double-checks this too, since I did it rather quickly.  It uses a BowtieHit for a specific hit:
/*  Stores the information from a single record of the bowtie map. A given read
    may have many of these.  Reads up to 255bp are supported.
*/
struct BowtieHit
{ ...

The whole structure can be seen here:
https://github.com/infphilo/tophat/blob/fb406c837accbf60e8b328f919ce8fe5e6a7d0c4/src/bwt_map.h#L75-143
Then for a read one has a vector of these:
struct HitsForRead
{
	HitsForRead() : insert_id(0) {}
	uint64_t insert_id;
	vector<BowtieHit> hits;
};

This is listed here:
https://github.com/infphilo/tophat/blob/fb406c837accbf60e8b328f919ce8fe5e6a7d0c4/src/bwt_map.h#L1033-1038
I haven't had much time to look carefully at STAR, though it's coded approach is understandably very different.
Paul

One of the drivers for the change is the need to be able to reconstruct the fragment information for reads mapping to smaller constructs like lncRNAs where having only the position of the matched read(s) will not be definitive enough.  Association with a fragmentId would allow the downstream user to link up the specific reads.  As currently defined, there are no 'verbs' for Fragment.  I'm an uncertain if the API should support a query for Fragment or leave it to the downstream user.  If a Fragment query is not to be supported then perhaps we don't need to have the definition.  Regardless, there is a need to match a read with its one or more mates by something more definitive than position alone.

I'd be happy to do another PR to add the Request and Response methods.

@saupchurch, I agree that without Fragment queries there's no point in adding a Fragment definition; what I'm not clear on is whether adding Fragment queries helps app developers enough to be worth the cost to server developers. Do you have any pointers to sample code that does the reconstruction you're describing (either an existing app that does it from BAM files, or a new app that does it by calling the GA4GH API)? If so, that would help understand if/how an API extension could help.

So continuing from before, now with STAR the story is more tricky.  Even though the programming is intriguing from one perspective - STAR seems to love global variables - and for many reasons let's try to make ours a little different.  For any implementation we will do, let's try to make our code as elegant as possible while also being efficient.  I'm sure among ourselves we've seen all possible variations of coding styles, so you know what I mean.  So without further ado, let's jump into the code:
The first thing to do is start here:
https://github.com/genome-vendor/star/blob/e1a11f890b3c72cb2bf380c74f652b3213acc1cd/Stats.cpp#L21-32
https://github.com/genome-vendor/star/blob/e1a11f890b3c72cb2bf380c74f652b3213acc1cd/Stats.cpp#L125-127
void Stats::addStats(Stats &S) {//add S to Stats
    readN += S.readN; readBases += S.readBases;
    ...
    mappedReadsU += S.mappedReadsU; mappedReadsM += S.mappedReadsM;
	...
}

void Stats::reportFinal(ofstream &streamOut, Parameters *P) {
 ...
    <<setw(w1)<< "MULTI-MAPPING READS:\n" \
               <<setw(w1)<< "Number of reads mapped to multiple loci |\t"      << mappedReadsM <<"\n" \
               <<setw(w1)<< "% of reads mapped to multiple loci |\t"           << (readN>0 ? double(mappedReadsM)/double(readN)*100 : 0)<<'%' <<"\n" \
 ...
}

Thus based on this we need to locate where the Stats are stored for reads to lead to incrementing mappedReadsM:
https://github.com/genome-vendor/star/blob/e1a11f890b3c72cb2bf380c74f652b3213acc1cd/ReadAlign_outputAlignments.cpp#L63-66
	    if (outFilterPassed) {
            if (nTr>1) {//multimappers
                statsRA.mappedReadsM++;
                unmapType=-1;
            } else if (nTr==1) {//unique mappers

Next we need to find where nTr get's increased and this can be found here:
https://github.com/genome-vendor/star/blob/e1a11f890b3c72cb2bf380c74f652b3213acc1cd/ReadAlign_multMapSelect.cpp#L24-48
...
nTr=0;
    for (uint iW=0; iW<nW; iW++) {//scan windows
        for (uint iTr=0; iTr<nWinTr[iW]; iTr++) {//scan transcripts
            if ( ( (trAll[iW][iTr]->maxScore + P->outFilterMultimapScoreRange) >= maxScore ) || \
                 ( chimRecord && trAll[iW][iTr]->iFrag>=0 && (trAll[iW][iTr]->maxScore + P->outFilterMultimapScoreRange) >=maxScoreMate[trAll[iW][iTr]->iFrag] )  ) {//record this alignment
                // if paired-end, record alignments from ALL windows
                if (nTr==MAX_N_MULTMAP) {//too many alignments for this read, do not record it
                    ostringstream errOut;
                    errOut  << "EXITING: Fatal ERROR: number of alignments exceeds MAX_N_MULTMAP, increase it and re-compile STAR";
                    exitWithError(errOut.str(), std::cerr, P->inOut->logMain, EXIT_CODE_PARAMETER, *P);
                };

                trMultScores[nTr]=trAll[iW][iTr]->maxScore;
                trMult[nTr]=trAll[iW][iTr];
                trMult[nTr]->Chr = trAll[iW][0]->Chr;
                trMult[nTr]->Str = trAll[iW][0]->Str;
                trMult[nTr]->roStr = trAll[iW][0]->roStr;
                if ( P->outSAMprimaryFlag=="AllBestScore" && trMultScores[nTr] == maxScore ) trMult[nTr]->primaryFlag=true;

                if ( (trAll[iW][iTr]->maxScore + P->outFilterMultimapScoreRange) >= maxScore) nTrMate++;

                nTr++;
            };
        };
    };
...

Then noticing trMult is probably what must be key, it then can be found here:
https://github.com/genome-vendor/star/blob/e1a11f890b3c72cb2bf380c74f652b3213acc1cd/ReadAlign.h#L95-96
...
       intScore trMultScores[MAX_N_MULTMAP];//scores for the multiple mappers
       Transcript* trMult[MAX_N_MULTMAP];//multimapping transcripts
...

So yes, this is another approach but ours is will be targetting a much bigger scale, which would require architecting it a little differently.
Hope it helps,
Paul

@dglazer, if space is an issue for indexing why not just optimize using coding schemes like Rice coding, Golomb coding, Gamma, Delta or Varint encoding as necessary for the task at hand (disk and/or wire optimizations)?  This is just a short list of coding schemes.  If we want to group multiple values, then we can use Group Varint encoding.  If speed is an issue then we have replicated index shards with balancers.  Some highly-accessed parts of the index can stay in memory and some on disk, so this can even be dynamically adjusted - which has parallels to the Memtable/SSTable approach.  Again many possibilities.


Is safe filter really supported

From docs

Django templating language is fully supported, including filters and tags.

Is that really true? At least safe filter does not seem to work?

safe generates code, which is not probably recognized by LO.

Seems linebreaks don't work too.


本地化时间(对使用SQLALCHEMY情况下)

将utcfromtimestamp改为fromtimestamp

can you elaborate the reason for the change?

when you click the tab 24hours,

it will show in UTC time if you use SQLALCHEMY as the profiler engine. But if you use other engines, it will show in your local time.By changing utcfromtimestamp to fromtimestamp, it will be solved.


Preventing transitions inflexible in 4.x

This is a continuation of https://github.com/ReactTraining/react-router/issues/4635 but in a new issue as that particular issue appears to be at a dead end.
Transition prevention seems to have a regression of functionality from version 2/3. The solutions put forward in the linked ticket work for simple use cases, but as has been said already, they are not sufficient for advanced cases such saving dynamic data prior to allow transition to continue.
For example, you can have access to a redux store with
export function makeHistoryUserConfirmation(store) {
  return function getUserConfirmation(message, callback) {
    // render some custom component into a completely different dom tree; not great.
    // When I'm at /user/profile/edit
    // I want to save/discard changes to that data prior to callback()

    // When I'm at /asset/edit
    // I want to save/discard changes to that data prior to callback()

    // Since this global function has no React application for rendering context,
    // all of the logic must be implemented imperatively inside of here

    if (store.isEditingProfileData) // ?? imperative

    if (store.iseEditingAssetData) // ?? imperative
  }
}

render(
  <ReduxProvider store={store}>
      <Router
        basename={i18n.basename}
        getUserConfirmation={makeHistoryUserConfirmation(store)}
      >
        <App />
      </Router>
  </ReduxProvider>,
  document.getElementById('app')
);

but since you're now out of the context of your <App /> component, you cannot declaratively render different components which are hooked into the store (which in this theory would handle saving of different data based on where the user is in the app). You would have to move all of the logic into the the one component you're rendering from within getUserConfirmation and do all of the logic imperatively. The rest of react-router 4's API is very declarative, but this is glaringly not so.
I don't actually have an API in mind right now (though I'm trying to come up with one), but I'd like to have this issue open to track ideas.

I don't mean this to be dismissive of the issue, but this really needs to live in history instead of here. This is because there is no longer a central route configuration ("static routing" as Ryan has coined it) and therefore no single transition to block. The singular action really lies not in the route transition, but the location transition. That's what you're attempting to block: sending your browser to another location. And history is now the sole arbiter of all location-related activities, so it's the best place to implement this kind of functionality.
history currently does implement such an API and we use it via <Prompt>. So if that API/implementation isn't sufficient (it certainly leaves a lot to be desired), we should open up issues over there to improve it.
Also, I understand this relies on imperative escape hatches. But it's unlikely we'll land on a declarative approach to this, since we are no longer hooking into the creation of React Elements and other weirdness. It's harder for us to build some APIs this way, but we think the overall API surface is better for it.

I actually think https://github.com/ReactTraining/history/pull/484 will allow this to be entirely solved in user-land. Appreciate the response and I'll reopen if that's not the case or if it turns out some decent API could actually land in the router. Thanks.


Use HELM readiness-check in progress tracker

Description
The HELM API is already including a Kubernetes client which includes the logic to wait for resources.
As consolidation of our internal Kubernetes API we shoul reuse the readiness-check for resources from HELM kubeclient in the progress tracker.
AC:

Progress tracker is using HELM readiness checks for measuring the progress of applied resources

Reasons
Verify how we can reuse the existing HELM API which has a higher maturity level compared to a custom implementation.
Attachments

Depends on #539

Functionalities of the Reconciler were migrated to the new architecture, this issue will not be worked on.


GROOVY-9292: Compilation error when accessing a protected super class…

… field from a closure using owner, delegate or thisObject qualifier (different package)

The PR is based on PR https://github.com/apache/groovy/pull/1046 and tweak a bit according to suggestions from @eric-milles .
As 72 hours has gone, I will merge the PR to avoid code conflicts.


Tab size depends on window width with "above" virtual text

Steps to reproduce

Run vim --clean
Source the following file:

set noequalalways
50vnew
28vsplit
call setline(1, "foo\tbar")
call prop_type_add('theprop', #{highlight: 'Special'})
call prop_add(1, 0, {'type': 'theprop', 'text': '12345', 'text_align': 'above'})

Tab size differs in the first and the second vsplit

Expected behaviour
Tab size is the same in the first and the second vsplit
Version of Vim
9.0.1628
Environment
Operating system: Arch Linux
Terminal: kitty
Value of $TERM: xterm-kitty
Shell: fish
Logs and stack traces
No response

See also / possibly duplicate of #12232
Only / always the first tab within a line is affected.


GE Omas - server implementation

Issue to track progress in GE server implementation

Closing this issue, will open finer grained issues connected to project https://github.com/odpi/egeria/projects/7


[Bug]: Automatic export of Better BibTeX keeps "Disabled" and can't be changed

Debug log ID
JGNMENI2-apse
What happened?
[Bug]: Automatic export of Better BibTeX keeps "Disabled" and can't be changed. After changing the status to "on Change" and then clicked OK, the setting keeps the same ("Disable") when opening the Preferences Windows again.
I restarted Zotero, but the problem is still here.

Can you

go into the hidden preferences
look for translators.better-bibtex.logEvents
double-click it to set it to true
try to change the setting to on Change
send a new debug log

I cannot read D<number> logs, only BBT logs, which end in -apse or -euc.

Sorry, here it is: MTJSPH9P-euc

Can you try whether this build fixes the problem for you?

Yes it works (for now at least)! Thanks!!


verify and read config file in two steps (#I53)

Coverage increased (+0.02%) to 93.931% when pulling 426a97ff6f23cb74d38c82c946681ea351496ada on volkerkochnovatec:I53 into 871ee5142f05f25d1d12d3c2c552cbd8728f9be7 on NovaTecConsulting:2.0.


Change go version to 1.21

Issue #, if available:
Description of changes:
Testing performed:
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

Codecov Report
Attention: Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.

Project coverage is 24.78%. Comparing base (d597e80) to head (57df474).

Files
Patch %
Lines

controllers/cloudstackmachine_controller.go
0.00%
2 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #374      +/-   ##
==========================================
- Coverage   25.66%   24.78%   -0.88%
==========================================
  Files          59       59
  Lines        5563     4760     -803
==========================================
- Hits         1428     1180     -248
+ Misses       3996     3455     -541
+ Partials      139      125      -14

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

Setting up environment failed

/approve
/lgtm

Test Results : (tid-491)
Environment: kvm Rocky8(x3), Advanced Networking with Management Server Rocky8
Kubernetes Version:  v1.27.2
Kubernetes Version upgrade from:  v1.26.5
Kubernetes Version upgrade to:  v1.27.2
CloudStack Version:  4.19
Template:  ubuntu-2004-kube
E2E Test Run Logs: https://github.com/blueorangutan/capc-prs/releases/download/capc-pr-ci-cd/capc-e2e-artifacts-pr374-sl-491.zip

Summarizing 3 Failures:
 [FAIL] When testing Kubernetes version upgrades [It] Should successfully upgrade kubernetes versions when there is a change in relevant fields
 /root/go/pkg/mod/sigs.k8s.io/cluster-api/test@v1.4.8/framework/machinedeployment_helpers.go:127
 [FAIL] When testing affinity group [It] Should have host affinity group when affinity is pro
 /jenkins/workspace/capc-e2e-new/test/e2e/common.go:348
 [TIMEDOUT] When testing machine remediation [It] Should replace a machine when it is destroyed
 /jenkins/workspace/capc-e2e-new/test/e2e/machine_remediation.go:59

Ran 27 of 30 Specs in 10784.817 seconds
FAIL! - Suite Timeout Elapsed -- 24 Passed | 3 Failed | 0 Pending | 3 Skipped
--- FAIL: TestE2E (10784.82s)
FAIL


pgsql (postgresql) error clean installation

Hi, using pgsql with fresh installation and getting datatables error.  Switching to mysql no problems.

@corepay we have used Raw MySQL queries in this application for grid part. you need to convert those to PGSQL.

Got it, thanks.  MySql is good for now.  Looks good though!


Fixed issue - php

Pull Request Type
What kind of change does this PR introduce?
[ ] Solved an issue/task
What is the current behavior?
array of 5 items
Issue Number: 1594
What is the new behavior?
Created a simple program that displays "Beef" to the console from the array provided.
Other information

Merged

This is an automated message from Fork, Commit, Merge [BOT].

Thank you for your contribution! Your pull request has been merged. The files have been reset for the next contributor.
What's next?
If you're looking for more ways to contribute, I invite you to check out our forkcommitmerge.io website repository. The repository contain real issues that you can help to resolve or create some of your own if you see any bugs or want to add new features to the site, etc. You can also check out the Influences section in the README to find more projects similar to this one.
Also please leave a star to this project if you feel it helped you, i would really appreciate it.
I look forward to seeing your contributions!


How do you delete an OAuth2 credential?

I've already deleted all consumers, but when I create a new consumer and try to add the same credentials to it, Kong tells me the credentials already exist. So presumably this is due to previous credentials not being deleted. I've tried doing a DELETE on http://localhost:8001/consumers/consumer-id/oauth2 but it tells me method is not allowed.
Any help would be greatly appreciated. Thanks!
P.S.
I think this is the same as #438, which I see has been closed 12 days ago. Does this mean the fix for this will be included in the next release?

Yes, this is exactly #438 and will be included in the next release. For now, if you deleted your consumers, I can only advise to cqlsh into the Cassandra cluster and run:
TRUNCATE oauth2_tokens;
TRUNCATE oauth2_credentials;
TRUNCATE oauth2_authorization_codes;

You cannot delete entire collections at once hence why the DELETE method does not work on that endpoint. But that still wouldn't work, you'd have to run the statements I described.

Ok thanks! Any estimate on when the next release would be @thibaultCha ? :)


Emerging issues typo corrected

Fixed the PowerShell command to start the services.

Approved

Reintroduced a spelling problem on StartType. It needs to be PascalCase or camelCase.


[QST] Merlin models support for PyTorch

❓ Questions & Help
Details
I have come across the following statement in the README file of the Merlin Models repository: "In our initial releases, Merlin Models features a TensorFlow API. The PyTorch API is initiated, but incomplete." This indicates that while there is some progress in implementing a PyTorch API for Merlin Models, it may not be fully functional or comprehensive at this time. right?
Considering this information, I would like to inquire about the current state of the PyTorch API for Merlin Models. Are there any updates or developments regarding its completeness and usability? If it is still a work in progress, is there an estimated timeline for when the PyTorch API will be fully supported?
Thank you for your attention to this matter. I look forward to your response.

@adhiiisetiawan thanks for your question. We are currently working on PyTorch API  code. It is not ready yet and it will take 1-2 releases to create the examples and documentation around the API usage.

Thank you for your response and providing an estimated availability for the PyTorch API.
I look forward to the future release that includes the PyTorch API, as it will greatly enhance the usability and compatibility of Merlin Models with PyTorch.


Stream_bath - pollWindow size in case of restart client application

Issue description
We are trying to implement storing progress in our cdc-consumer-service using the inbuilt progress manager(provided by scylla-cdc-go). But after the cdc-consumer-service and restarting it, we are unable to receive any more cdc updates.
However, according to the logs the progress is loaded for the last_timestamp(check screenshot attached).
On further checking the library code, we noticed that this could be happening because inside the getPollWindow() function in stream_batch.go, the queryWindowRightEnd and confidenceWindowStart are very far apart. On printing the queryWindowRightEnd, we found this value to be equal to the current_generation value(2021-08-04 05:42:32.878000+0000 - progress table screenshot attached) and confidenceWindowStart= time.Now().
Because of this huge size window we are not receiving cdc updates.
On changing this window value to a small one(say 1second - by hard coding), it is working fine.
So I believe the value of queryWindowRightEnd in getPollWindow() function is not getting set to the appropriate value. Are we missing something here?###hat this could be happening because inside the getPollWindow() function in stream_batch.go, the queryWindowRightEnd and confidenceWindowStart are very far apart. On printing the queryWindowRightEnd, we found this value to be equal to the current_generation value(2021-08-04 05:42:32.878000+0000 - progress table screenshot attached) and confidenceWindowStart= time.Now().
Because of this huge size window we are not receiving cdc updates.
On changing this window value to a small one(say 1second - by hard coding), it is working fine.
So I believe the value of queryWindowRightEnd in getPollWindow() function is not getting set to the appropriate value. Are we missing something here?

We have seen a similar behavior reported before https://scylladb-users.slack.com/archives/C2NLNBXLN/p1632379210266400
In short, after we restart a consumer with progresstable, unprocessed stream_ids will start polling from the generation's start and, with very small QueryTimeWindowSize values, this may cause it to take a VERY LONG TIME to catch up, specially with a very old stream generation.
A way to "workaround" it is to increase QueryTimeWindowSize to something like 24h, but it may not be an ideal approach for everybody.
I think the issue/report should be a programmatic way to allow specifying the start Poll time (at user own's risk), instead of polling from the starting generation for unprocessed stream_ids. This will help development/non-write-heavy workloads to catch up faster when polling unprocessed stream IDs.
FYI @piodul @haaawk

FYI @avelanarius.
@piodul and @avelanarius let's have a meeting to find a common solution for both Golang and Java

Please note I've addressed the issue with persisting CDC log reader state + restart behaviour in https://github.com/scylladb/scylla-cdc-go/pull/10.

And I also would be interested to help with Java lib + scylla-cdc-source-connector where I'm suspecting similar issues (but even harder to debug/analyse...).

@AdamStawarz , could you please update if your issue was resolved by #13


Create graph nodes to represent database tables

Sample level quality control data (FastQC, Flagstat, Vcfstats) is stored in CloudSQL database tables. It's not easy to trace the provenance of data from GCS -> CloudSQL right now. Also, not easy to know where these tables live. I think it would be good to represent these data stores in the graph.

Basic graph model:
graph TD
    qaTable[Quality Assessment Table] -- INSERTED_INTO --> dbTable[Database Table]
    db[Database] -- HAS_TABLE --> dbTable

Cypher query to create Database Table & Database nodes:
MERGE (db:Database {name: ${database_name})
ON CREATE SET
  db.private_ip_address = ${private_ip}
  db.vcpus_count = ${vcpus}
  db.memory_gb = ${memory}
  db.storage_gb = ${storage}
  db.software = ${software}
  db.version = ${version}
  db.zone = ${zone}
  db.network = ${network}
MERGE (db)-[rel:HAS_TABLE]->(dbTable:DatabaseTable {name: "fastqc"})
ON CREATE SET
  db.schema = ${table_schema}
RETURN db, rel, dbTable

Challenge in connecting the qa table to the db table is there is no obvious mapping. The logs from Cloud SQL aren't going to know anything about the source file that the data was read from. Maybe I can connect the logs to the Trellis job and then connect the job to the input... and then that input to the database table.
First, I need to see what the logs for CloudSQL operations look like.

CloudSQL logs don't appear to show anything related to database operations. Logs just show automatic housekeeping logs: "automatics analyze of table" and "automatic vacuum of table".

Alternative solution is to just send the DatabaseQueryRequests from the function, as the operations are performed. I think this is fine and it has the advantage that the function knows both ends of the operation: source object and database/table.

I also realized that the implementation of the postgres-insert-data function includes a design pattern that runs counter to the rest of Trellis. Inserting QC data into the Postgres database is handled by that function, but the operation is tracked in Neo4j as a Job node. In every other instance, a Job node refers to an operation that was performed on a virtual machine using a Docker image and a scheduler. Operations that are performed by Trellis functions are not tracked in the database because they aren't considered "jobs", since they aren't transforming data. Here, the data isn't being transformed but it is being loaded into the database; so, should this be considered a Job, should it have a new label, or should it just be an invisible internal Trellis operation?


Include lib64 for virtualenv

On systems that require a lib64, virtualenv creates a symlink to the local lib (see fix_lib64).
A fresh virtualenv with the current .gitignore template lists lib64 as the only unchecked change.

Thanks!


Accept txids, block hashes, and outputs in search box

Block hashes and txids are both 64 hex digit hashes, so will have to be disambiguated by querying bitcoind. Outputs are TXID:VOUT, so can be transformed into /output/TXID:VOUT.

Fixed by #549.


included python dev instruction

Whenever I set this up on a new machine, I noticed that I will need to apt-get python-dev in order to get the Python.h library, and simply added this instruction to the README.

Thanks for the PR! Updated in the wiki


refactor,chore(egen) : refactored code according to template guidelines

This PR includes
1.Adds Colab authentication and kernal restart steps.
2.Adds colab enterprise logo with link.
3.Removes IS_TESTING condition.
4.Replace REGION with LOCATION.
5.Removed UUID code
6.added missing code and removed unused modules
7.added required libraries in installation section
REQUIRED: Fill out the below checklists or remove if irrelevant

If you are opening a PR for Official Notebooks under the notebooks/official folder, follow this mandatory checklist:

[x] Use the notebook template as a starting point.
[x] Follow the style and grammar rules outlined in the above notebook template.
[x] Verify the notebook runs successfully in Colab since the automated tests cannot guarantee this even when it passes.
[x] Passes all the required automated checks. You can locally test for formatting and linting with these instructions.
[ ] You have consulted with a tech writer to see if tech writer review is necessary. If so, the notebook has been reviewed by a tech writer, and they have approved it.
[ ] This notebook has been added to the CODEOWNERS file under the Official Notebooks section, pointing to the author or the author's team.
[x] The Jupyter notebook cleans up any artifacts it has created (datasets, ML models, endpoints, etc) so as not to eat up unnecessary resources.

/gcbrun

/gcbrun

/gcbrun


2.3.alpha3 export to IOS fails in xcode with AR-related undefined symbol errors

Godot version: 3.2.alpha3.official
OS/device including version: OSX Catalina 10.15
Issue description:
After grabbing export templates for 3.2.alpha3, an 'export project' works without error. Upon compilation within xcode 11.1 using iOS SDK v13.1, compilation fails with the following stack trace.
Undefined symbols for architecture arm64:
  "_OBJC_CLASS_$_ARSession", referenced from:
      objc-class-ref in fugitive.a(arkit_interface.iphone.opt.debug.arm64.o)
  "_OBJC_CLASS_$_ARWorldTrackingConfiguration", referenced from:
      objc-class-ref in fugitive.a(arkit_interface.iphone.opt.debug.arm64.o)
ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

I'm looking for both a mitigation and possibly a bug fix in the exported code, if we determine that is indeed a cause of this.
Steps to reproduce:

Run v3.2.alpha3.official of godot.
Export for IOS using the downloaded export templates.
Open exported .xcodeproj in xcode 11.
Build
above error hit here

Note that I didn't select ARkit capabilities (or any others) when checking boxes in the export template.

#33406 duplicate.


handle undefined routes (404)

Currently we just display a blank page (probably some javascript exceptioning somewhere).
We should either create a 404 page or redirect users to root.

@blukai do you want to design what that 404 page looks like? I can route to a generic 404 but maybe you can come up with something cool? I'll assign this one to myself unless @howardchung was planning on doing it.

Go ahead.  Here's the current page: https://www.opendota.com/404

ugh, there's no way to do this in react-router natively (at least as far as I can tell). I can probably make something work but it won't be super simple.

Can you use a wildcard route placed at the end?

yes, I didn't read the docs very thoroughly.

@mike-robertson Sure, I'll come up with something.
As the basis I prefer clone of /components/Home
✌

Ok, I just have some simple div with text in it, it will render inside of the app component (header and footer will be included).


Support for alpine with aarch64

I am trying to run an application that runs inside an alpine container that runs on aarch64 (aws graviton nodes)
I am getting this exception:
Caused by: java.lang.Exception: No native library found for os.name=Linux-Alpine, os.arch=aarch64, paths=[/usr/lib/jvm/java-1.8-openjdk/jre/lib/aarch64/server:/usr/lib/jvm/java-1.8-openjdk/jre/lib/aarch64:/usr/lib/jvm/java-1.8-openjdk/jre/../lib/aarch64:/usr/java/packages/lib/aarch64:/lib:/usr/lib]
It seems that there is support for Linux-Alpine but only for x86. Could we add Linux-Alpine aarch64 as a target?

I see dockcross now has musl versions of most of the arm images, I will try those and see if I can make it work.

I created a PR to fix this.
Since xerial is on leave and won't merge this soon you could try to build it yourself. Just clone my PR, and run mvn package.

Wow thanks for the quick response here. I'm not working over the holiday but I'll try it out next week.

This looks to be working for me. Thank you very much!


use XmlWritter to avoid serialising Xml Declaration in csproj

the idea is to have the minimum amount of change detected in csproj
<?xml version ...?>
as never been part of csproj

Will merge it this weekend and release a new NuGet package!

Thanks! Thats great!


Support Windows paths in compilation-mode

The regexps added to compilation-error-regexp-alist-alist need to match paths
output by Bazel, which are subject to numerous constraints.  As currently
written, this does not support Windows paths, which, as output by Bazel, start
with a drive letter and a root path (e.g C:/).
Address this by extending the regexp to account for Windows paths.  UNIX-style
path processing should not be affected; tests passed there.
NOTE: I was not able to build the test suite on Windows, nor do there seem to be
instructions for doing so.  I'll be happy to discuss what I tried in the
PR, but I'm not exactly a Windows expert, nor do I currently do development on it regularly.

LGTM, thanks!
For now don't worry about running the tests on Windows, I still need to make rules_elisp work on Windows.


Deprecate and remove node-local-dns annotations which already have a Shoot spec field replacement

How to categorize this issue?

/area networking
/kind cleanup
What would you like to be added:
This issue proposes deprecation and removal of the following annotations:

alpha.featuregates.shoot.gardener.cloud/node-local-dns - it is possible to enable/disable the node-local-dns from the Shoot spec (.spec. systemComponents. nodeLocalDNS.enabled)
alpha.featuregates.shoot.gardener.cloud/node-local-dns-force-tcp-to-cluster-dns - the corresponding Shoot spec field is .spec. systemComponents.nodeLocalDNSforceTCPToClusterDNS
alpha.featuregates.shoot.gardener.cloud/node-local-dns-force-tcp-to-upstream-dns - the corresponding Shoot spec field is .spec. systemComponents.nodeLocalDNSforceTCPToUpstreamDNS

We have to first deprecate these annotations. We can use API warnings to let the Shoot owners know that these annotations are deprecated.

Switching on node-local-dns via shoot specification will roll the nodes even if node-local-dns was enabled beforehand via annotation.

Why is this needed:
To have a cleaner API.

FYI @ScheererJ @DockToFuture

/assign


Set up Discovery Engine secret for search-admin

We will soon want to wire up search-admin to GCP Discovery Engine ("Vertex AI Search") in the same way we have done for search-api-v2. This integration will allow Search Admin to modify some resources on Discovery Engine to allow administrative users from the wider GOV.UK search team to make some modifications to configuration through the Search Admin UI.

Add external secrets template for search-admin Discovery Engine configuration
Update app config values to retrieve secrets as environment variables (in integration only for now to test it out)

The secrets have already been created in search-v2-infrastructure: https://github.com/alphagov/search-v2-infrastructure/blob/main/terraform/environment/discovery_engine.tf#L77


Issue with  tag

Hi,
It looks like there is a typo at https://github.com/timcreative/bootstrap-wizard/blob/master/index.html#L134.
It should be Street Name not <labe>Street Name; l is missing.

@akshaybabloo thank you for the information. We just updated it.
Best,
Alex


⚠ Bofrost.de has degraded performance

In cc46c09, Bofrost.de (https://www.bofrost.de) experienced degraded performance:

HTTP code: 200
Response time: 1412 ms

Resolved: Bofrost.de performance has improved in 469d544.


Does this project identifies the unknown user as "Not Enrolled"

Hi @manishpandit I have two questions to ask

I was trying to run the project but the error:
File "cnn_test.py", line 23, in
X, Y = voxforge.get_test_data()
File "/home/sanat/Desktop/Audio Comparizon/Neuralshizz/code/voxforge.py", line 140, in get_test_data
return get_data("X_Test", "Y_Test")
File "/home/sanat/Desktop/Audio Comparizon/Neuralshizz/code/voxforge.py", line 116, in get_data
create_h5_file()
File "/home/sanat/Desktop/Audio Comparizon/Neuralshizz/code/voxforge.py", line 94, in create_h5_file
X_Train, Y_Train, X_Dev, Y_Dev, X_Test, Y_Test = data_from_files()
File "/home/sanat/Desktop/Audio Comparizon/Neuralshizz/code/voxforge.py", line 67, in data_from_files
X_All = X_All[permutation].reshape(X_All.shape[0], X_All.shape[1], X_All.shape[2], 1)
IndexError: tuple index out of range

What is the issue in this?

Does this code recognizes the unknown people i.e. Not Enrolled people
ex: It should display
abc.wav =  not enrolled/Unknown
john.wav = John
.
.
.etc

Can you please help me with this? Thanks in advance !!!

Sanat,
I have re-worked the entire project in jupyter notebook. Please take a look if you are still interested.
This application only predicts from known users.


dozer-proto improvements

Add unit tests for map
Update Protobuf library to 3.3.0
Remove generated sources

@jbq ; can you fix checkstyle please

checkstyle is OK, the problem now is that an outdated version of protoc is installed on Travis

@jbq ; not sure what you mean by that. Isn't the problem travis fails due the fact you've deleted ProtoTestObjects.java - which is generated, but you don't seem to have changed anything to re-generate it from proto.
https://github.com/DozerMapper/dozer/blob/master/proto/src/test/java/org/dozer/propertydescriptor/ProtoFieldPropertyDescriptorCreationStrategyTest.java#L39-L41

Recent changes:

Use protoc-jar maven plugin
Run license:format on generated Java source file to make travis happy

Seems allright now.

@jbq ; The code looks fine, i just have a few questions about how you are using mvn to build.
@orange-buffalo ; can you also review please.

Here's how to build:
mvn -f bom-dependencies/pom.xml install
mvn -f proto/pom.xml test-compile
cd proto
mvn test

@jbq ; thats my point. If i am a first time user, i need to run several commands, which instantly puts me off contributing to the project.
I want to keep it simple and follow a standard maven dev flow of;
mvn clean install
If the protoc can be activated by a profile, then this solves that problem.

Hi @garethahealy, a few things worth to explain:

the extra install step that I suggested in bom-dependencies is because I understood you were not able to build the proto module.  This is because you have a previous version of bom-dependencies installed in your local Maven Repo with an outdated protobuf version.  To solve this for other developers we just need to bump version 6.1.0-SNAPSHOT to let's say 6.1.1-SNAPSHOT
the extra install steps in Travis is just because of the license check, no more.  The generated Protobuf Java source file has no license header of course, and it is enforced by the plugin so I artificially insert the header during build to make Travis happy
with this update protoc is taken from a JAR file, which is more plug and play for developers, there's no need to install protobuf on the developer workstation anymore

@orange-buffalo I went ahead and applied your suggestions.  Thanks, it's simplier than ever!  The only thing is the plugins are specific to the proto module so I didn't move them to plugins-parent otherwise they will be applied to all modules.
I'm looking forward to see this PR merged, so that #416 (support for snake case fields) can also be incorporated.
Also, please consider bumping the current version 6.1.0-SNAPSHOT to eg 6.1.1-SNAPSHOT to make sure developer working copies continue to build flawlessly.  I haven't included that change to this PR.

@jbq ; plugins-parent controls the versions, as per [1]. So its safe to replace the older plugin with the one you've suggested. This means you then dont need to specify the plugin version in the proto pom.
[1] https://github.com/DozerMapper/dozer/blob/master/plugins-parent/pom.xml#L188-L193

Hi @garethahealy I think I did what you advised, please verify


Take care of some old todos

Summary
Details and comments
Fixes #

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.01%) to 56.766%

Totals

Change from base Build<PHONE_NUMBER>:
-0.01%

Covered Lines:
2043

Relevant Lines:
3599

💛  - Coveralls

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.01%) to 56.766%

Totals

Change from base Build<PHONE_NUMBER>:
-0.01%

Covered Lines:
2043

Relevant Lines:
3599

💛  - Coveralls


CQ-4350121 Added missing inner repeatability tests.

Description

Related Issue

Motivation and Context

How Has This Been Tested?

Screenshots (if appropriate):
Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

[ ] I have signed the Adobe Open Source CLA.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[ ] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes and the overall coverage did not decrease.
[ ] All unit tests pass on CircleCi.
[ ] I ran all tests locally and they pass.

Closing this PR, cherry-picked the commit in my pr https://github.com/adobe/aem-core-forms-components/pull/471
cc:- @sakshi-arora1


minimp3: remove TAG+ support

It's a still-born extension that no one uses, no player supports, and no tag library parses.
And it's not impossible to hit it as a false positive..
(The removal has already been suggested to mainstream at https://github.com/lieff/minimp3/issues/66)

If https://github.com/mackron/dr_libs/issues/263 doesn't get  resolved and we won't go back to dr_mp3, please merge this and also cherry-pick to SDL3 branch as well.

I went ahead and merged and cherry-picked.


Extend the m365 status command with appId and tenant

We should extend the output of the m365 status command with information about the appId and tenant used in authentication.
We should extend the output from:
{
  "connectedAs": "name"
}

to:
{
  "connectedAs": "name",
  "appId": "123",
  "appTenant": "common"
}

Rationale
After experimenting with a custom AAD app, today, while trying to create an app reg using the CLI, I got an "Insufficient privileges to complete the operation" error. After scratching my head for a sec I realized, that it's because the app reg I was using yesterday had no scopes for managing AAD apps. That's not obvious when you check status, because it only shows the user or app name. Unless you know to check the token, it's not trivial to figure out and is something that we should communicate more clearly.

Awesome! Let's ship it.

We also have a isAppOnlyAccessToken function, to me it looks useful to also add this to the status?
{
  "connectedAs": "name",
  "appId": "123",
  "tenant": "common",
  "isAppOnlyConnected": true
}

We'd get tenant information from the login configuration rather than from the token. We want to show the tenant to which the app belongs rather than the tenant to which you signed up. Which brings up a good point that we should clarify it, and use appTenant rather than just tenant which is ambiguous in this context.
As for the app only, I'm not sure if that won't be clear when you look at connectedAs and see it contain app name rather than a UPN.

Yeah exactly!

What if we used not isAppOnlyConnected but rather show the value of the authType option that was used during login? It would not only allow you to determine if you're using app-only or not but could possibly support other scenarios as well.

Not sure what you mean here. Is the tenant name stored somewhere while logging into the CLI?

Yes, we store the information along tokens. We're serializing the instance of the Service class and have access to its properties https://github.com/pnp/cli-microsoft365/blob/1e08e6ce84efcbb4a65f1c96998588a5b3420a98/src/Auth.ts#L37-L51. You can get to it via auth.service.

What if we used not isAppOnlyConnected but rather show the value of the authType option that was used during login? It would not only allow you to determine if you're using app-only or not but could possibly support other scenarios as well.

Sounds great to me, however this is already being logged when using the --debug flag. Should I also log it when not running it in debug mode?
https://github.com/pnp/cli-microsoft365/blob/1e08e6ce84efcbb4a65f1c96998588a5b3420a98/src/m365/commands/status.ts#L30-L36

Good catch! Which brings us to a good point: should this additional information be visible always or only in debug mode (because that's typically when you'd need it)?

I think it's a great and useful addition to always show 😊


Set up pre-commit linting hooks

This still will not add workspaces. Also I hope workspaces aren't exclusive to Yarn 2. We are using Yarn 1, and I tried to move to Yarn 2, but it was such a mess, Yarn 1 seemed a lot friendlier than whatever they turned it into, so I don't want to make the switch.

Workspaces are available since Yarn v1.0. Do you want me to add them here or in a different PR (if we decide to use them)?

Preferably a different PR


Messages sent to file sns differs when previewing the messages to be sent ('Messages being sent to nowhere')

Details here:
https://jira.jpl.nasa.gov/browse/PODAAC-5820

This is most likely due to us using threads and parallel processing of the granules. We can't guarantee the order in which the messages are sent or how many of each footprint, tig, dmrpp.
if you are previewing each footprint, tig, dmrpp individually at the same time then it should look the same. If were mixing footprint, tig, and dmrpp it will probably look different as when we are in preview messages aren't being sent the threads are running faster through each granule and can yield different results on whats being sent.

@sliu008 Maybe we should add an output when in preview mode saying like:
NOTE:  When in preview mode, the messages sent count may not be accurate since it's only simulating sending messages.
What you think?