Error in Authentication_Score

Hi everyone,
I can't find my way around this error and would greatly appreciate your help.
Error in rule Authentication_Score:
    jobid: 1289
    input: results/MALT/MST2_055_m.trimmed.rma6, results/AUTHENTICATION/MST2_055_m/2483404/MaltExtract_output/log.txt, results/AUTHENTICATION/MST2_055_m/2483404/name_list.txt
    output: results/AUTHENTICATION/MST2_055_m/2483404/authentication_scores.txt
    log: logs/AUTHENTICATION_SCORE/MST2_055_m_2483404.log (check log file(s) for error details)
    conda-env: /aMETA/aMeta/.snakemake/conda/f662868e1efffa191f0ae26f948c8cee_
    shell:
        Rscript /Bioprograms/aMETA/aMeta/workflow/scripts/score.R results/MALT/MST2_055_m.trimmed.rma6 $(dirname results/AUTHENTICATION/MST2_055_m/2483404/MaltExtract_output/log.txt) results/AUTHENTICATION/MST2_055_m/2483404/name_list.txt $(dirname results/AUTHENTICATION/MST2_055_m/2483404/name_list.txt) &> logs/AUTHENTICATION_SCORE/MST2_055_m_2483404.log;
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

It happens with all taxid entering that part. Then the log contains the following:
Error in if (sum(df$V4 > 3)/dim(df)[1] > 0.1) { :
  missing value where TRUE/FALSE needed
Execution halted

Thanks in advance.

Hi @renatolatorre !
I have two questions in order to see in which direction we could investigate.

Do you use mobaxterm and have you opened the script plot.R with it? When mobaxterm saves files, it reformats them and then the quotes don't look the same etc and the code doesn't work anymore.
Could you check if the results/AUTHENTICATION/{sample}/{taxid}/PMDscores.txt were generated for the species for which the error arises? And do these files look fine?

@renatolatorre I believe (as @ZoePochon says) that there was not PMDscores.txt file generated for that taxid. It can also be that the file is there but empty, so division by dim(df)[1] diverges. Please check this. In any case, thanks for reporting, we should have a closer look at this soon.

Hi, thanks for the replies. I don't use mobaxterm. I use Ubuntu on Windows to connect to a server and didn't try to open the R script before the errors. Also, at the time I checked that PMDscores.txt were generated for the taxid with errors and contained information inside.
During these days I managed to finish running aMETA by restarting it several times when the error arised. I think when restarting, by chance it started and finished with other jobs before going to that authentication step

Seems to be related to the issue #161, I am working on it, should be fixed in the new PR

Fixed in the latest PR


add goimports (or gofmt)

another analysis tool that should be added:
goimports -d
https://godoc.org/golang.org/x/tools/cmd/goimports

gofmt provides similar output, but maybe not as good http://goinbigdata.com/goimports-vs-gofmt/

The vast majority of the editor will format the code, this is not goreporter focus.

the majority of editors will also lint the code and/or do other static analysis...
my perspective is that if the developer hasn't configured their editor correctly (because that still needs to manually be done, goimports doesn't come automatic), these results can be included as one of the points of data that get evaluated during a pull request

"A Golang tool that does static analysis, unit testing, code review and generate code quality report"
code formatting does in fact sound like the focus of this tool

Thank you very much,I will consider adding this feature to it in the future. If you are willing to work with me to develop goreporter, that would be better.


Update issue templates

 Here is an overview of what got changed by this pull request:

Issues
======
- Added 20

See the complete overview on Codacy


fix memory leak in ws client

if the write fails then an error is returned but the sub still exists in the map with no way to clear it
sub objects are pretty large which leads to a significant memory leak on repeated calls with write failures

thank you!


emmet code hint window display appears delay

emmet code hint window display appears 5 sec late after typing tag

Can you attach a screencap showing the issue?


Support passing scalars by reference to ctypes/cffi methods

Some external libraries expose methods that require passing scalars by reference (instead of by value). It would be good to support this in numba as well.
When using ctypes, this could use ctypes.byref.
In [1]: import ctypes

In [2]: libc = ctypes.CDLL("libc.dylib")

In [3]: i = ctypes.c_int()

In [4]: f = ctypes.c_float()

In [5]: s = ctypes.create_string_buffer(b'\000' * 32)

In [6]: print(i.value, f.value, repr(s.value))
0 0.0 b''

In [7]: libc.sscanf(b"1 3.14 Hello", b"%d %f %s", ctypes.byref(i), ctypes.byref(f), s)
Out[7]: 3

In [8]: print(i.value, f.value, repr(s.value))
1 3.140000104904175 b'Hello'

cffi doesn't expose object types for pointers, but an equivalent example is:
In [26]: import cffi

In [27]: ffi = cffi.FFI()

In [28]: ffi.cdef("int sscanf ( const char * s, const char * format, ...);")

In [29]: C = ffi.dlopen(None)

In [30]: i = ffi.new("int *")

In [31]: f = ffi.new("float *")

In [32]: C.sscanf(b"1 3.14", b"%d %f", i, f)
Out[32]: 2

In [33]: i[0]  # cffi uses indexing with 0 as dereference
Out[33]: 1

In [34]: f[0]
Out[34]: 3.140000104904175

Numba may want to expose its own pointer/ref type to allow use with both ctypes and cffi wrapped functions.

@jcrist thanks for suggesting this and helping to improve Numba. I have labelled this as a 'fetaure request' for the time being.


Bug in Export as Python script

Bug: Notebook Editor, Interactive Window, Editor cells

Steps to cause the bug to occur

Launch a new or existing notebook with code and markdown
Click "Export as" and select Python Script

Actual behavior
The cell marker for markdown in the exported script file appears as
null.tpl [markdown]
# ## heading

Expected behavior
In version v2020.9.112786 the output python script appears as follows
# %% [markdown]
# ## heading

Your Jupyter and/or Python environment
Please provide as much info as you readily know

Jupyter server running: Local
Extension version: v2020.9.114305
VS Code version: 1.50.0
Setting python.jediEnabled: false
Setting python.languageServer: Microsoft
Python and/or Anaconda version: 3.7 and 3.8
OS:  Mac
Virtual environment: conda

Python Output
> pyenv root
> python3.7 ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> python3.6 ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> python3 ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> python2 ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> ~/Applications/miniconda3/envs/hv5/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import sys;print(sys.executable)"
> ~/Applications/miniconda3/bin/conda info --json
Starting Microsoft Python language server.
> ~/Applications/miniconda3/bin/conda env list
Python interpreter path: ~/Applications/miniconda3/envs/hv5/bin/python
> ~/Applications/miniconda3/bin/conda env list
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import jupyter"
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import notebook"
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter kernelspec --version
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py vscode_datascience_helpers.daemon --daemon-module=vscode_datascience_helpers.jupyter_daemon -v
> ~/Applications/miniconda3/envs/hv5/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir ~/Desktop/t -s --cache-clear
cwd: ~/Desktop/t
Error 2020-10-10 11:25:54: Failed to parse discovered Test [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
> ~/Applications/miniconda3/bin/pytest --version
Error 2020-10-10 11:25:54: Python Extension: displayDiscoverStatus [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py -c "import nbconvert"
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python (daemon) -m jupyter nbconvert /var/folders/lk/s__7f9fx15x_zrw6q5xkmm500000gp/T/079a338f-17a4-4099-bc8e-d7e892f4ed32/tmp-24986s97W0AoEEAEI.ipynb --to python --stdout --template /var/folders/lk/s__7f9fx15x_zrw6q5xkmm500000gp/T/tmp-24986TD26cET8TVOb.tpl
> ~/Applications/miniconda3/envs/hv5/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir ~/Desktop/t -s
cwd: ~/Desktop/t
Error 2020-10-10 11:28:09: Failed to parse discovered Test [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
> ~/Applications/miniconda3/envs/hv5/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir ~/Desktop/t -s
cwd: ~/Desktop/t
Error 2020-10-10 11:28:12: Failed to parse discovered Test [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
Starting Microsoft Python language server.
Python interpreter path: ~/Applications/miniconda3/envs/data/bin/python
> ~/Applications/miniconda3/bin/conda info --json
> ~/Applications/miniconda3/bin/conda info --json
> ~/Applications/miniconda3/envs/data/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py discover pytest -- --rootdir ~/Desktop/t -s --cache-clear
cwd: ~/Desktop/t
Error 2020-10-10 11:28:14: Failed to parse discovered Test [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
> ~/Applications/miniconda3/bin/pytest --version
Error 2020-10-10 11:28:14: Python Extension: displayDiscoverStatus [r [Error]: Traceback (most recent call last):
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/run_adapter.py", line 17, in <module>
    from testing_tools.adapter.__main__ import parse_args, main
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/__main__.py", line 9, in <module>
    from . import pytest, report
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/__init__.py", line 7, in <module>
    from ._discovery import discover
  File "/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/testing_tools/adapter/pytest/_discovery.py", line 8, in <module>
    import pytest
ModuleNotFoundError: No module named 'pytest'

	at ChildProcess.<anonymous> (/Users/adefusco/.vscode/extensions/ms-python.python-2020.9.114305/out/client/extension.js:9:53541)
	at Object.onceWrapper (events.js:313:26)
	at ChildProcess.emit (events.js:223:5)
	at ChildProcess.EventEmitter.emit (domain.js:475:20)
	at maybeClose (internal/child_process.js:1021:16)
	at Process.ChildProcess._handle.onexit (internal/child_process.js:283:5)]
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python ~/.vscode/extensions/ms-python.python-2020.9.114305/pythonFiles/pyvsc-run-isolated.py jupyter nbconvert --version
> ~/Applications/miniconda3/envs/plot/bin/python (daemon) -m jupyter nbconvert /var/folders/lk/s__7f9fx15x_zrw6q5xkmm500000gp/T/45b5a54d-be0e-40be-b683-0045c063ac6b/tmp-24986ZT61YC7tA6Bk.ipynb --to python --stdout --template /var/folders/lk/s__7f9fx15x_zrw6q5xkmm500000gp/T/tmp-24986TD26cET8TVOb.tpl

Microsoft Data Science for VS Code Engineering Team: @rchiodo, @IanMatthewHuff, @DavidKutu, @DonJayamanne, @greazer, @joyceerhl

I have similar issue https://stackoverflow.com/questions/64297352/issue-with-vscode-jupytoer-notebook-editor

Hi @AlbertDeFusco, thanks for highlighting this. I can repro this bug. I've put up a fix to correct this and the bug fix will be available in our next release. Thanks again for bringing this to our attention!
@cliu268, the bug you linked to is a separate issue—would you mind filing a new issue with more details on your Python environment so that we can assist you: https://github.com/microsoft/vscode-python/issues/new?labels=type-bug%2C+data+science&template=1_ds_bug_report.md Many thanks!

Thanks @joyceerhl the issue appears to be with python 3.9 and I found some documented solution here https://discuss.codecademy.com/t/having-trouble-installing-jupyter-notebooks/537292
I am reverting back to 3.7 for now.


Support mutiple inputs of keras modek.predict.

Support mutiple inputs of keras modek.predict. It works along with #996 and fix #939

The code doesn't work.
Just copy pasting the example for multi results in "Argument 1: cannot convert from '(Tensorflow.NumPy.NDArray, Tensorflow.NumPy.NDArray)' to 'IDatasetV2'
.
Any ideas?


Must Specify at least one message

Hello,
I have this configured, got my botfather thing set up, got the chat ID, config is all happy in Homebridge... but when I reboot I get an error in the Log
[Telegram] Initializing Telegram Platform...
[Telegram] TelegramPlatform Plugin Loaded
[Telegram] Found bot in config: "Telegram"
Error: Must specify at least one message for telegram notifications.
etc etc

Can you post your config.json?


Including newrelic and CLS together overwrites your custom CLS data

I am having an interesting issue.  CLS was created for commerical pursuits for newrelic.  I have newrelic and like it.  You gracefully open sourced the app.  I want to use CLS and newrelic.  Each time I include both newrelic and CLS the newrelic library wipes my CLS stores out.  There are no naming conflicts.

@askhogan This sounds like a question for @hayes -- It could be as simple as making sure that newrelic is required before continuation-local-storage in your application, or there could be some deeper conflict between the two. I'm no longer up to speed with how New Relic uses (or doesn't use) CLS, and so the only bits I can help you with are the pieces that are CLS-specific.
Michael, what's the story here? Do I need to do something to shim CLS to avoid getting stepped on by newrelic? Or is my advice above enough?

I can't think of any reason that would be happening.  I am curious what version of newrelic you were using.  If there is some kind of conflict I would like to get that fixed right away.  There was an issue we had with modules that used an older version of async-listener, but I don't think CLS has used that in a long time.

newrelic  "version": "1.16.1"
continuation-local-storage   "version": "3.1.2",

I use CLS in my logger file to add context like username and organization so I can pinpoint what user is affected.  I use newrelic for the transaction traces.

I am not sure what is causing this, but I would recommend trying it with<EMAIL_ADDRESS>

+1, using newrelic==1.22.0.

Although I cannot add much detail, I can say I had the exact same problem. Eventually I had to give up on New Relic.

I'm having the same problem using loopback. Can't use new relic on my loopback application because of cls
Related to https://github.com/strongloop/loopback/issues/1984

Seeing the same issue
continuation-local-storage: 3.1.6
newrelic: 1.25.4
Any chance the problem is because newrelic treats cls as a bundled dependency? Could that be causing node to load two different versions of cls?

This issue happens on Node 4.3.1 for me, but downgrading to Node 0.12.10 fixed it.
@ianwremmel which Node version are you using?

I've used 4.3.0 and 4.3.1. I think I fixed it by requiring cls right before newrelic.

Hey, I am having a newrelic-cls issue too:
the following code:
// require('newrelic');
const CLS = require('continuation-local-storage');
const Express = require('express');
const app = Express();
const Ns = CLS.createNamespace('ns');
app.get('/', (req, res) => {
    Ns.run(() => {
        Ns.set('a', 1);
        Promise.resolve()
            .then(() => {
                console.log(Ns.get('a'));
                return '100'
            })
            .then((response) => {
                console.log(Ns.get('a'));
                return res.json(response);
            });
    });
});

app.listen(8080, () => {
    console.log('ok');
});

outputs on request:
1
1

But if I uncomment the import of newrelic, I get:
1
undefined

I'm using the latest versions of the CLS and of newrelic. I'll try to dig that tomorrow, but if anybody has a clue of where it comes from.. I assume it is the wrapping of Promises by newrelic that causes the issue.

Probably the double-wrapping hides the __asl_wrapper property attached here: https://github.com/othiym23/async-listener/blob/master/index.js#L450
@hayes Might know better.

I saw the same with appdynamics code. Requiring CLS first fixed the issue for me.

As I am bundling the CLS into a RASP solution, it is hard to ensure the clients declare newrelic after sqreen.

@vdeturckheim I'd have to investigate the newrelic and AppDynamics agents to be sure, but I believe that the fact that this works with one order and not the other means that the APM agents aren't as careful about leaving the wrapped functions in a state where they can be wrapped again later. If this is the case, then the issue is with them, rather than CLS, and there's little that CLS can do about it. This is why the documentation for CLS (and, when it used CLS as an enabling module, the newrelic agent) was so insistent about it being loaded first. If you can't get newrelic and other agents to change, perhaps you can partially remedy the problem by making clear what needs to happen in our own docs?
I wish I had a better solution for you here, but these are the wrinkles come from having a technique that relies upon extensively monkeypatching the core platform. (And the reason why newrelic probably doesn't follow the rules is the same reason it abandoned using CLS – reduced overhead and increased performance, which are important requirements for a monitoring solution intended to be run in production.)

@othiym23 thanks a lot for this clear answer. This outcome is the one I have been suspecting for a while!
Ageed regarding the fact that the issue is on NewRelic side. In the past, requiring sqreen before newrelic caused a few issues in NewRelic but they are fixed now. So we'll go this way.
Thanks again for this great module and your answer!


[Button] Remove style-propable mixin from flat-button-label

All good :+1: :grin:

@newoga Thanks!


fix overlap issue

Fixes #63
Please consider it in Hactoberfest

Ill Review Your Code.... For Now Ill label it As hactoberfest-accepted


Update package.json to anonymise my email

Just got notified my email is in here due to https://github.com/ericblade/quagga2/commit/96f7b30e7b850c06096213f1c318921cb9c850a5, so here's a PR to anonymise it.

Thanks for the PR!  Have a great day


UI refactor

This refactor mainly involved converting all Angular controllers to use the 'controllerAs' syntax in order to avoid scope problems and to bring older controllers in line with newer ones.  It also removes unnecessary files and commented lines of code.  It touches a lot of files so on-site testing will be necessary.

Tested this on-site and fixed the only issue I found.

I tested for a while and didn't notice any issues using the static data.

No issues found. Looks good to merge.


[#33] Fix python excludes

We excludes all python files that contains "lib", "doc", and "bin" in their path. This is a bug since we only wanted to exclude "python/bin/", "python/lib/", and "python/doc/*". This PR fixed the bug and made some code refactors of listPythonBinaries.

LGTM! ending tests


Drop after_help in generate-lockfile

From reviewing the history this looks like a copy-paste error while
porting to clap (https://github.com/rust-lang/cargo/pull/5152): this is
fetch's after_help info
Fixes #5692

:hourglass: Testing commit 7ef6976e1d945cf6b9fd4aaadf60e9405e6305fc with merge 773e3b6c6bd68dc6f50c612d6331f928fa818965...

:sunny: Test successful - status-appveyor, status-travis
Approved by: alexcrichton
Pushing 773e3b6c6bd68dc6f50c612d6331f928fa818965 to master...


Move to version supporting node 4.x

    THRIFT-9999: [Move to version supporting node 4.x]
    Client: [lib/nodejs]

Pretty sure we already support node.js 4.x.


Tag autocompletion

Added autocomplete feature for tags

https://trello.com/c/lISxt3n9/153-adding-new-tags-doesn-t-allow-for-multiple-comma-delimited-tags-assignment-in-one-go

This looks good. However, I would request that tags which are already selected below should not appear in the autocompletion options.

Added that feature in ^


browsing: we should allow pdf and json export (as in logged mode)

at the moment the export buttons ofr pdf and json are hidden in browsing mode, but only editing should be banned.

Fixed by this commit actually: 2170d8965c353455d5bd6c38dee1603823ccf982

done


Rename AStar.get_points() to AStar.get_point_ids() for clarity

The same has been done for AStar2D as well.
If desired, I could open a PR against the 3.2 branch to update only the method descriptions.
This closes https://github.com/godotengine/godot-docs/issues/3515.

Thanks!

Thank you!


Elf Saving Throws tables are wrong

Their values are completely wrong. Also there's a typo on the Known Spells value for level 7

Moving to dcc-content, this is for the DCC system.


Type 'T' is not assignable to type when Generic Anonymous Function is inside an interface.

Bug Report

🔎 Search Terms
Generic Anonymous Function inside Interface
Type 'T' is not assignable

🕗 Version & Regression Information
Appears to be an error on all versions back to atleast 4.0.

This is the behavior in every version I tried, and I reviewed the FAQ for entries about this.

⏯ Playground Link

Playground link with relevant code
💻 Code

interface GenericFnContainer {
    fn: <T>(a: T) => any
}

const a: GenericFnContainer = { fn: (a: string) => "a" };

🙁 Actual behavior
Type '(a: string) => string' is not assignable to type '<T>(a: T) => any'.
  Types of parameters 'a' and 'a' are incompatible.
    Type 'T' is not assignable to type 'string'.

🙂 Expected behavior
This shouldn't be an error, as the generic in this function is string. I might've stumbled onto a known bug, or maybe I'm using this syntax wrong? I'm not sure.

Consider the following code.
fn2(1) is a legal call because <T>(a: T) => any can receive anything. But (a: string) => "a" can only receive string type input, and it will cause a runtime error.
const fn1: (a: string) => string = function (a) {
  return a.toLowerCase();
}

// @ts-ignore-error
const fn2: <T>(a: T) => any = fn1;

fn2(1);


sphinx build fails with Unicode encode/decode error (and insufficient context from build)

Details
I have problems with the RTD builds of my project.

Project: python-behave
Build #: 3813119 (and earlier, version: latest)

Error:
'ascii' codec can't encode character u'\ufffc' in position 80: ordinal not in range(128)
Note that my normal sphinx-builds show no problem at all.
Wiping the "latest" and "stable" versions on "readthedocs.org" did not help.
It would be much easier if you would provide more details (like a stack trace) to identify the problem location (at least for the project admin).

It seems you somehow added an invisible ASCII code into the conf_py_file (\ufffc) variable when you set it on your project. This caused us to generate an invalid path to your conf.py which contained unexpected Ascii.
Should be fixed now.

Thanks.


adds tolerations, nodeSelector, and affinity to trillian.

Partly resolves https://github.com/sigstore/helm-charts/issues/696

Description of the change
Adds tolerations, nodeSelector and affinity to charts.

Existing or Associated Issue(s)

Request for tolerations, nodeSelector and affinity to be allowed to configure for all charts
Additional Information

initial PR w/ all changes in one.
Checklist

[x] Chart version bumped in Chart.yaml according to semver. Where applicable, update and bump the versions in any associated umbrella chart
[x] Variables are documented in the values.yaml and added to the README.md. The helm-docs utility can be used to generate the necessary content. Use helm-docs --dry-run to preview the content.
[x] JSON Schema generated.
[x] List tests pass for Chart using the Chart Testing tool and the ct lint command.

❯ ct lint --config ct.yaml
Linting charts...

------------------------------------------------------------------------------------------------------------------------
 Charts to be processed:
------------------------------------------------------------------------------------------------------------------------
 trillian => (version: "0.2.23", path: "charts/trillian")
------------------------------------------------------------------------------------------------------------------------

"sigstore" already exists with the same configuration, skipping
Linting chart "trillian => (version: \"0.2.23\", path: \"charts/trillian\")"
Checking chart "trillian => (version: \"0.2.23\", path: \"charts/trillian\")" for a version bump...
Old chart version: 0.2.22
New chart version: 0.2.23
Chart version ok.
Validating /Users/x308080/Projects/helmcharts-2/charts/trillian/Chart.yaml...
Validation success! 👍
==> Linting charts/trillian
[INFO] Chart.yaml: icon is recommended

1 chart(s) linted, 0 chart(s) failed

------------------------------------------------------------------------------------------------------------------------
 ✔ trillian => (version: "0.2.23", path: "charts/trillian")
------------------------------------------------------------------------------------------------------------------------
All charts linted successfully

changed the following to get tests to pass:
"storageClass": {
                    "type": ["string", "null"]
                    },
"envCredentials": {
                    "type": ["string", "null"]
                    }

cc @hectorj2f / @cpanato

job failed i will fix it

k, i will rebase the remainder PRs.


When I was packing, I encountered the following situations? Did any friends meet?

ERROR in static/js/vendor.4f122ca48b271b7a79f2.js from UglifyJs
Unexpected token: punc ()) [./~/vue-json-excel/dist/vue-json-excel.esm.js:190,0][static/js/vendor.4f122ca48b271b7a79f2.js:69084,16]

that workd for me:
https://stackoverflow.com/a/43674989


Bump Presto versions + adopt Flink versions

Remove Flink 1.14 for Iceberg/master
Add Flink 1.17 for Iceberg/master
Set Flink default to 1.15
Add combinations for Iceberg 1.2
Add Presto 0.280

Bump Spark from 3.3.1 to 3.3.2

Recent failure against Iceberg/master https://github.com/projectnessie/nessie/actions/runs/4649898865/jobs/8228561733?pr=6546


[v4.y] Test VERIFY_PEER / VERIFY_NONE work against real cluster

Followup to https://github.com/ManageIQ/kubeclient/pull/540.  (It fixed https://github.com/abonas/kubeclient/issues/525 which was only broken on master, not v4.y, but good to have these tests here too.)
Adding tests that Client honor VERIFY_PEER/VERIFY_NONE by connecting to the temporary cluster during test/config/update_certs_k0s.rb script.
They are skipped during a regular rake test so they will NOT run in CI.
(Can we run docker --priviledged in github actions?)

Ooh, exciting!  Yes, it can run in CI.

[ ] it failed with SSL errors differing from what I expected :tada:
https://github.com/ManageIQ/kubeclient/runs/5346969200?check_suite_focus=true#step:6:60

[ ] Should switch to docker.pkg.github.com/k0sproject/k0s/k0s so GitHub actions don't hammer docker hub.

OK pin-pointed the timeout:
KubeclientRealClusterTest#test_real_cluster_verify_none = 1.15 s = .
KubeclientRealClusterTest#test_real_cluster_verify_peer =
Error: Process completed with exit code 124.

Probably exercise_watcher_with_timeout, which suggests .finish on watches is generally not as reliable as I believed :-(

@russell @grosser @agrare I still need to tackle the runaway test ^ but please review the general direction.
I want real end-to-end tests of when TLS verification actually verifies, and the setup here of starting a real cluster works surprisingly fast and opens the door to many more future real-cluster tests...


I cannot test workspace functionality on the edit assistant page

Because we removed all the menu options from the chat pane on the edit assistant page, I cant test workspace functionality. I specifically want to test how vision worked and couldnt. i had to go to chat. this could be a hinderance for building certain types of agents.

im not sure what we should do, so if you pick this up, speak with me first.


added dsm0.github.io to index.html

would love to be a part of this project : )

Incomplete PR.

Incomplete PR.

Sorry, forgot to add webring.
Also, I'll spruce up my site before I open another PR.


feature(curated-syllabi): update redirect

Changes
Fixes https://github.com/Qiskit/platypus/issues/1684
Implementation details

when a user copies a syllabus, they are redirected to the syllabus/edit/<SYLLABUS-CODE> form

updated the form so the Syllabus name persists with the "Copy of [Original syllabus name]" convention
keeps the first field (Syllabus name) in focus, so the user has an indication of what they just duplicated

Screenshots
https://user-images.githubusercontent.com/6276074/200942415-38c491fe-1bfb-4cc2-891f-d79edb0bb851.mov

@vabarbosa
That's a great point...
I thought about that, but it's too early to tell if we should clear it or not.
I pseudo-tested this by clearing it locally, then tried to put myself in the experience of a new user, and I could totally see a user missing that field, only to realize later when they want to hit "Publish", that they need to go back up and fill in their Instructor name.
My guess is that if a user is prompted to rewrite the title field, they'll notice hey, I'm not Peter Shor... and since I'm editing the Syllabus title, let me go ahead and update the rest of the fields
(✋🏼 this is definitely an assumption)
Still, I think it's too early to know either way.
I'd vote ship what we have here, and if we need to clear it, we can make a new PR?


Running Median

Description
I want to contribute a very famous problem of Data Structures and Algorithms named - The Running Median, which focuses on calculating the median for a continuous stream of numbers.
For Example -
Input -
6  /*total numbers in continous stream */
6 2 1 3 7 5
Ouptut -
6 4 2 2 3 4
Explaination -
S = {6}, median = 6
S = {6, 2} -> {2, 6}, median = 4
S = {6, 2, 1} -> {1, 2, 6}, median = 2
S = {6, 2, 1, 3} -> {1, 2, 3, 6}, median = 2
S = {6, 2, 1, 3, 7} -> {1, 2, 3, 6, 7}, median = 3
S = {6, 2, 1, 3, 7, 5} -> {1, 2, 3, 5, 6, 7}, median = 4
Note - We have to print only the integer part of the median.
@ujjwalban @miraj0507 Kindly assign this problem to me as a part of the GSSOC'22 contribution.
Domain
Data Structure
Type of Contribution
Addition
Code of Conduct

[X] I follow Contributing Guidelines & Code of conduct of LearnCPP.

@iamgunjan @miraj0507 Kindly assign this issue to me so that I can work on it as soon as possible, Thank you.

kindly type /assign to self assign it

/assign

/assign


WIP: Integration tests

Tests covering majority of the recent UI flows are provided.
Depends on:

[x] #117 Cypress
[x] #119 camelCase fix

TODO (please do not merge yet):

[x] ISO downloading
[x] Host role selection
[x] Host enable/disable
[x] NICs table on ClusterDetail
[ ] Cluster Configuration Page
[ ] Start installation and Abort installation

Bugs found and not fixed immediately (follow-up needed):

Cluster list status value should be capitalized (first letter)
Missing "Delete cluster modal" (feature missing)

Rebased


create push, deploy, and test scripts for AWS EKS

We have an ECR to push our container images ( public.ecr.aws/h8y1n7y7 )
It’s a public registry because our images are public anyway; there’s nothing to hide.
I’ve hacked a demo branch for a quick demo to use those images:
https://github.com/vmware-tanzu/secrets-manager/tree/ovolkan/demo
In the demo branch, I renames the "local" k8s manifests to point to ECR by simply renaming their image: values
And I also used the following script to push things to ECR:
#!/bin/bash

# Set your ECR repository base URI
ecr_base_uri="public.ecr.aws/h8y1n7y7"

# Logging in to ECR
#aws ecr get-login-password --region us-west-2 | docker login --username AWS --password-stdin $ecr_base_uri
aws ecr-public get-login-password --region us-east-1 | docker login --username AWS --password-stdin public.ecr.aws/h8y1n7y7

# Looping through Docker images
docker images | grep "0.22.4" | grep "localhost" | awk '{print $1 ":" $2}' | while read image
do
    # Extract repository name from image name
    repo_name=$(echo $image | cut -d '/' -f 2)

    # Tag the image with the ECR URI
    ecr_image_uri="$ecr_base_uri/$repo_name"
    docker tag $image $ecr_image_uri

    # Push the image to ECR
    echo "Pushing $ecr_image_uri ..."
    docker push $ecr_image_uri

    # Optional: check if you want to remove local image after push
    # docker rmi $image
    # docker rmi $ecr_image_uri
done

That’s good and all for a demo;  yet, what would even be better is to push the "next version" (v0.22.4 in this case) to ECR and have scripts to setup, teardown, deploy, and test the images on ECR
The benefits of this would be, we can provide public images to those who want, with a disclaimer that they are edge versions, they are not a release cut, and they shall be treated as such.
Another benefit (for me, Volkan) is that I can keep ECR as a relatively stable demo environment (for various stakeholders) and use the build server for (comparatively unstable) CI automation.
Right now how I do this is to hack make deploy-local
(since the local manifests point to remote images in the branch; make deploy-local deploys images from ECR)
Upon completion of this feature the expectation is:

make k8s-manifets-update will create ecr k8s manifests along with local and remote.
make deploy-ecr will deploy VSecM using the ecr images.
make push-ecr will push images from the local registry to ECR.
make test-ecr will run test using the example images that are on ECR.
make clean should work as it did before and if the kube context is pointing to EKS; it should clean things there.

Done.


chore(event_list): 12482 - short state for event_list panel

How it looks:

Design solution:
create ShortPanel component. Make short content rely on currentEventResourceAtom
Question to reviewer:
is that a good solution? Possible options - add eventListResourceAtom (then what's the priority to pick event), rely solely on eventListResourceAtom (i think it's wrong because not all events are in event list - old events has links and can be reached through currentEventResourceAtom)

i will resolve merge conflict after fix of main branch expected from @vkozio
it's only for translations anyway

Regarding architecture:
I see that currentEventResourceAtom returns event with geometry, but event list use just events.
Do you need event with geometry for short panel?
Because we have currentEventAtom that is updated from different places like autoSelectEvent. And for loading you can reuse loading prop from EventsListPanel, because whole list is loaded even in short panel mode.

to @propakov:
We sure don't need geometry in analytics
Problem with current event atom is that it only returns event id, but i need more event info. Possible solution is to

Get current event id
Try find it in event list
If no result - get data from currentEventResourceAtom

Is that enough?

to @propakov: We sure don't need geometry in analytics Problem with current event atom is that it only returns event id, but i need more event info. Possible solution is to

Get current event id
Try find it in event list
If no result - get data from currentEventResourceAtom

Is that enough?

Looks good, but it would be weird if you'll have event loaded in resource in shortPanel and don't have it when switch back to the list, isn't it? Or it's what we need?

Reopening to trigger CI


removing func install

Just learned while testing out some KEDA stuff that the func tools deploy an older version of KEDA.  Have an issue with the core tools team to fix, but in meantime preparing this in case we don't want to bubble up while it'sg etting sorted out.

Too bad but we can re-add it later on indeed!


[Update] RTL v0.10.1

https://twitter.com/RTL_App/status/1363582174587465729?s=20

Just noting here that need to test with the Terminal, likely needs a port change in the config to make Loop work.
https://github.com/rootzoll/raspiblitz/issues/1993

A new optional feature in RTL is to add support for the boltz.exchange api ehich needs to have the boltzd running:
https://lnd.docs.boltz.exchange/en/latest/

Merged with #1994 which contains v0.10.0 .. will update to v0.10.1

OK RTL 10.0.1 tests looking good ... keeping open for final release testing.


TAJO-1704: Apply ComparableTuple to *AggregateExec.

Just rebased.

+1
LGTM! :-)

Hi @hyunsik
Could you explain why you changed queries and results for window function test?

@hyunsik are you working on this issue? If not, please close this PR. We can open again when we need later.

closed. Thank you.


Invoice HTLC shards should not remain in ACCEPTED state after cancelation

Background
As currently designed in the invoices RPC: invoices enter an ACCEPTED state when HTLCs are held but not yet settled with the preimage. This is designed to allow a caller to know when HTLCs are safely held and that they can settle with a preimage.
However if the preimage is never provided, the HTLCs will never leave this ACCEPTED state even though after a timeout they will no longer be able to be claimed
Ideally the surfaced state of the HTLC would indicate a different state to the RPC caller to disambiguate between "able to be settled" and "no longer able to be settled"
Your environment

LND 0.12.0-beta

Related: https://github.com/lightningnetwork/lnd/issues/4587
The original idea was to create a watcher that cancels back these htlcs right before the time out. That will also prevent the channel from force-closing. In that case, probably no new rpc state is needed.

The original idea was to create a watcher that cancels back these htlcs right before the time out. That will also prevent the channel from force-closing.

Seems we can just extend the existing invoice expiry watcher to add hodl invoices, but with a slightly different expiration value?
Actually why isn't that sub-system already handling this case?

So there are indeed three things to watch for:

invoice expiry
mpp release
hodl invoice release

Actually why isn't that sub-system already handling this case?

I don't remember exactly why we didn't use the invoice expiry watcher for mpp releases. Maybe it had to do with certain data not being available easily.

Had deeper look at this, and I think that the only case we're not covering is when the htlc goes to chain and then the timeout expires (which would be the case for hodl invoices that we fail to cancel, or a regular invoice when we hit chain between accept and settle). @alexbosworth do you remember if you've specifically seen this for invoices that are resolved on chain?
When we timeout an incoming htlc on-chain (1/2), we just mark the resolver as complete without signalling back to the invoice that we can no longer settle the invoice, so the htlcs stay open. We deliver updates to invoices (manual settle/fail) uni-directionally from invoices -> contractcourt through the hodlSubscriptions notification system. Options to address this could be:

Introduce a block based invoice expiry watcher which cancels these htlcs when their expiry height is reached (could also prevent force-close for hold invoices, perhaps on an opt-in basis)
Establish contractcourt -> invoice registry communication which cancels the invoices once they're expired on chain

I believe they resolved on-chain and the timeout expired

Linking related issue https://github.com/lightningnetwork/lnd/issues/4587

Should note not only did they expire the funds also were pulled back via the timeout path


detail view works with custom shelf books now

Description
Custom Shelf book to detail works
Trello card: https://trello.com/c/NsyqqgdM/66-library
Type of change

[x] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)

Change Status

[x] Complete, tested, ready to review and merge

How Has This Been Tested?

[x] Manually tested with simulator (iPhone 11 Pro Max)

Checklist

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[x] My changes generate no new warnings
[x] There are no merge conflicts

 Book Details


UI does not open in browser (does work on Tor)

I tried opening Mutiny in my browser from services in StartOS using the .local address but I get an alert telling me site cannot be reached and that I should check if there is a typo. There isn't, obviously but I get this at the bottom:
DNS_PROBE_FINISHED_NXDOMAIN
I have gone into this using a tor browser and using the .onion address but I would like to use the .local as well.
Anyone had this issue and how do I fix?

I am not too sure here, sounds like a networking issue for the start9 team

Yes, I think it’s actually a Start9 issue after a bit of thinking.
On Thu, Apr 11, 2024 at 03:23, benthecarman @.***(mailto:On Thu, Apr 11, 2024 at 03:23, benthecarman < wrote:

I am not too sure here, sounds like a networking issue for the start9 team
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @.***>


Issue with taking the backup of Windows Runtime deployment.

Hi,
We have enabled the backup prepare node in ERT and took the backup of Bosh Director and CF-xxxxx deployment successfully.
Now, when we try to take the backup of Windows Runtime deployment we are getting the following error:
[root@ashaplt00006 releases]# BOSH_CLIENT_SECRET=xxxxxxxxxxxxxxxxxxxxx \
>   bbr deployment \
>   --target 100.xx.xx.31 \
>   --username bbr_client \
>   --deployment p-windows-runtime-f9a69795cba9982868ef \
>   --ca-cert /home/openplatform/root_ca_certificate \
>   pre-backup-check
[bbr] 2017/07/31 04:11:55 INFO - Running pre-checks for backup of p-windows-runtime-f9a69795cba9982868ef...
[bbr] 2017/07/31 04:11:55 INFO - Scripts found:
Deployment 'p-windows-runtime-f9a69795cba9982868ef' cannot be backed up.
1 error occurred:
error 1:
failed to find instances for deployment p-windows-runtime-f9a69795cba9982868ef: ssh.NewConnection.ParseAuthorizedKey failed: ssh: no key found

[root@ashaplt00006 releases]#

Please help us to solve this issue.
Thanks,
Akhilesh Appana

Thanks for letting us know. This issue looks like a backup issue for ERT, can you please contact Pivotal support.


stress-ng: 0.06.14 -> 0.09.46

Motivation for this change
Package update
+ should be multi-platform
+ added build inputs recommended upstream
See: http://kernel.ubuntu.com/git/cking/stress-ng.git/plain/README
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[ ] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[x] Tested execution of all binary files (usually in ./result/bin/)
[ ] Determined the impact on package closure size (by running nix path-info -S before and after)
[x] Fits CONTRIBUTING.md.

$ ./result/bin/stress-ng --cpu 4 --vm 2 --hdd 1 --fork 8 --switch 4 --timeout 5m --metrics-brief
stress-ng: info:  [11495] dispatching hogs: 4 cpu, 2 vm, 1 hdd, 8 fork, 4 switch
stress-ng: info:  [11495] successful run completed in 300.36s (5 mins, 0.36 secs)
stress-ng: info:  [11495] stressor       bogo ops real time  usr time  sys time   bogo ops/s   bogo ops/s
stress-ng: info:  [11495]                           (secs)    (secs)    (secs)   (real time) (usr+sys time)
stress-ng: info:  [11495] cpu               63197    300.05    216.18    141.30       210.62       176.78
stress-ng: info:  [11495] vm              1330056    300.02    125.27     71.72      4433.17      6751.90
stress-ng: info:  [11495] hdd             1413827    300.36      0.80     78.57      4707.16     17813.12
stress-ng: info:  [11495] fork             356007    300.00     53.90     62.94      1186.69      3046.96
stress-ng: info:  [11495] switch         47303035    300.00     32.37    373.77    157676.69    116469.78

Success on aarch64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
cp -rp example-jobs/*.job /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46/share/stress-ng/example-jobs
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46
shrinking /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46/bin/stress-ng
gzipping man pages under /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46/share/man/
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46/bin
patching script interpreter paths in /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46
checking for references to /build in /nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46...
/nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46

Success on x86_64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
cp -rp example-jobs/*.job /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46/share/stress-ng/example-jobs
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46
shrinking /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46/bin/stress-ng
gzipping man pages under /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46/bin
patching script interpreter paths in /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46
checking for references to /build in /nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46...
/nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46

@GrahamcOfBorg build stress-ng

Success on aarch64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
/nix/store/v08nag15sbdjd1y3vhxh7sfkapb46bd3-stress-ng-0.09.46

No attempt on x86_64-darwin (full log)
The following builds were skipped because they don't evaluate on x86_64-darwin: stress-ng
Partial log (click to expand)

a) For `nixos-rebuild` you can set
  { nixpkgs.config.allowUnsupportedSystem = true; }
in configuration.nix to override this.

b) For `nix-env`, `nix-build`, `nix-shell` or any other Nix command you can add
  { allowUnsupportedSystem = true; }
to ~/.config/nixpkgs/config.nix.

Success on x86_64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
/nix/store/dcbg05mgf101yzn4j56yz6b97jy4j4fi-stress-ng-0.09.46

@GrahamcOfBorg build stress-ng

Success on aarch64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
cp -rp example-jobs/*.job /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46/share/stress-ng/example-jobs
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46
shrinking /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46/bin/stress-ng
gzipping man pages under /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46/share/man/
strip is /nix/store/p9akxn2sfy4wkhqdqa3li97pc6jaz3r1-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46/bin
patching script interpreter paths in /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46
checking for references to /build in /nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46...
/nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46

Failure on x86_64-darwin (full log)
Attempted: stress-ng
Partial log (click to expand)
Undefined symbols for architecture x86_64:
  "_getentropy", referenced from:
      _shim_getrandom in shim.o
ld: symbol(s) not found for architecture x86_64
clang-5.0: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [Makefile:350: stress-ng] Error 1
make[1]: Leaving directory '/private/tmp/nix-build-stress-ng-0.09.46.drv-0/stress-ng-0.09.46'
make: *** [Makefile:337: all] Error 2
builder for '/nix/store/lr7893vvqp9idq95xfwldmv07ll9gki7-stress-ng-0.09.46.drv' failed with exit code 2
error: build of '/nix/store/lr7893vvqp9idq95xfwldmv07ll9gki7-stress-ng-0.09.46.drv' failed

Success on x86_64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
cp -rp example-jobs/*.job /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/share/stress-ng/example-jobs
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46
shrinking /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/bin/stress-ng
gzipping man pages under /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/bin
patching script interpreter paths in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46
checking for references to /build in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46...
/nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46

For future reference, this is the Darwin failure:
shim.c:276:9: warning: implicit declaration of function 'getentropy' is invalid in C99 [-Wimplicit-function-declaration]
        return getentropy(buff, buflen);
               ^
1 warning generated.
[...]
LD stress-ng
Undefined symbols for architecture x86_64:
  "_getentropy", referenced from:
      _shim_getrandom in shim.o
ld: symbol(s) not found for architecture x86_64
clang-5.0: error: linker command failed with exit code 1 (use -v to see invocation)

It seems similar to this Python issue but stress-ng.h already contains :
#if defined(__APPLE__)
#include <sys/random.h>
#endif

Don't know much about Darwin so for now I'll just revert to marking this package Linux-only.

Success on aarch64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
/nix/store/i66gp5yza5hfq0phkbp1shkvi8bqi6v6-stress-ng-0.09.46

Success on x86_64-linux (full log)
Attempted: stress-ng
Partial log (click to expand)
cp -rp example-jobs/*.job /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/share/stress-ng/example-jobs
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46
shrinking /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/bin/stress-ng
gzipping man pages under /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/share/man/
strip is /nix/store/vcc4svb8gy29g4pam2zja6llkbcwsyiq-binutils-2.30/bin/strip
stripping (with command strip and flags -S) in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46/bin
patching script interpreter paths in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46
checking for references to /build in /nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46...
/nix/store/458w4f6l3ddfy1b5wv88hwqcpyjmg48y-stress-ng-0.09.46

@c0bw3b getentropy was added in 10.12, we use a whitelist of symbols available from 10.10->10.14 to make sure binaries built on the latest version are compatible with older releases and the other way around.
With https://github.com/NixOS/nixpkgs/pull/47678 we'll probably drop support for <10.12 making it available, that should fix this issue.

Thanks @LnL7 for the explanation. I'll retry adding Darwin support in a later update then.


Remove version: MonkeysAudio.MonkeysAudio version 1.019

[Automated] It returns code over 400 in all urls
Microsoft Reviewers: Open in CodeFlow

URL: https://monkeysaudio.com/files/MAC_1019.exe
Response status code does not indicate success: 404 (Not Found).
(Automated message - build 694)


B-19887: Add pricing estimate column to MTO Service Items

Agility ticket
Summary
In this story the pricing_estimate column is being added to mto_service_items table.
How to test

Run the migration scripts
Check the mto_service_items table for the pricing_estimate column

New column pops up for me locally!
First time I've done this as a requested change but since I thought of it - can you update the DB tracking spreadsheet? Then I'll get you the green stamp!
@traskowskycaci  Done


Search Provider : Yelp Search

It would help to search anything with Swirl on Yelp

PR merged, closing this issue.  Thank you for the contribution!

Hello @erikspears  Thanks for your help, as this issue and PR was created under hacktoberfest would this be counted under hacktoberfest and will I get any rewards?


Question about [GO] and [s]

Hi, thanks for your amazing work.
When you convert the label using class TokenLabelConverter, you pad the label with [GO] which is ignored during loss calculation, however in paper, figure 4 shows that the label is padded with [s].
Does this make any difference on accuracy?

[GO] is the start token. After the predicted text, succeeding tokens are spaces that are represented by [s].


segfault-handler breaks cross-architecture build

The introduced usage of segfault-handler breaks our cross-architecture build.
We didn't find any way on rebuilding segfault-handler to work in a AWS Lambda function expect the way of using a docker image. As this would introduce a lot of refactoring of our CI pipeline we decided to remove segfault-handler in our fork.
The AWS Lambda fails with:
ERROR	Error: /var/task/node_modules/segfault-handler/build/Release/segfault-handler.node: invalid ELF header
    at Object.Module._extensions..node (internal/modules/cjs/loader.js:1188:18)
    at Module.load (internal/modules/cjs/loader.js:986:32)
    at Function.Module._load (internal/modules/cjs/loader.js:879:14)
    at Module.require (internal/modules/cjs/loader.js:1026:19)
    at require (internal/modules/cjs/helpers.js:72:18)
    at bindings (/var/task/node_modules/bindings/bindings.js:112:48)
    at Object.<anonymous> (/var/task/node_modules/segfault-handler/index.js:3:37)
    at Module._compile (internal/modules/cjs/loader.js:1138:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:1158:10)
    at Module.load (internal/modules/cjs/loader.js:986:32)

Just to add more issues about segfault-handler package:
The library has some issues when running in Alpine Linux images:
https://github.com/ddopson/node-segfault-handler/issues/70
https://github.com/ddopson/node-segfault-handler/pull/67
Looks like they are not maintaining that package anymore.

Yah, got it. I'll do another release without this dependency.


fix: pass flag to default function

@W-11868418@

The WI mentions sf env create scratch --help doesn't show the default values --wait and --duration-days, which don't use a default function for these values. Is there any follow up work for it to work?
https://github.com/salesforcecli/plugin-org/blob/main/src/commands/org/create/scratch.ts#L86-L103

I tested plugin-org locally with @salesforce/sf-plugins-core": "2.2.10-beta.1

@peternhale QA looks good (tested with org commands, wait default and and devhub flags (were working before, tested to confirm it didn't break).
e2e test fail on latest node (linux and windows), I re-ran the jobs yesterday and also tested locally with node v20 and can repro the failure.

@peternhale QA looks good (tested with org commands, wait default and and devhub flags (were working before, tested to confirm it didn't break).
e2e test fail on latest node (linux and windows), I re-ran the jobs yesterday and also tested locally with node v20 and can repro the failure.

I'll install 20 and see what is up.
Thank you


fix: suppress error of no matching autocommands

There are cases where the error message "No matching autocommands" is shows.
So I added a placeholder for the autocommand.
I rejected the method of adding silent to doautocmd because it has side effects.
Or there was a way to check with exists(), but I chose this simple implementation.
Problem
The following error message is shows.
No matching autocommands: User DDCReady

Expected
No error message is shows.
Reproduce
testvimrc
set nocompatible

set rtp^=path/to/denops.vim
set rtp^=path/to/ddc.vim

call ddc#enable()

Run vim -u testvimrc.

The same issue exists for ddu.vim.

The same issue exists for ddu.vim.

Fixed.


adding the reject task indicator for thread pool burying point（#11706)

adding the reject task indicator for thread pool burying point

Codecov Report

Merging #11916 (b7d7967) into 3.2 (92421ba) will decrease coverage by 0.20%.
The diff coverage is n/a.

:exclamation: Current head b7d7967 differs from pull request most recent head a609a14. Consider uploading reports for the commit a609a14 to get more accurate results

@@             Coverage Diff              @@
##                3.2   #11916      +/-   ##
============================================
- Coverage     69.24%   69.04%   -0.20%
+ Complexity      340        2     -338
============================================
  Files          3299     1547    -1752
  Lines        154929    64021   -90908
  Branches      25776     9341   -16435
============================================
- Hits         107274    44204   -63070
+ Misses        38212    15550   -22662
+ Partials       9443     4267    -5176

see 1788 files with indirect coverage changes
:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

fix #11788


Add config "sentinel auth-pass" to entrypoint-sentinel.sh

Fix these job https://github.com/OT-CONTAINER-KIT/redis/pull/47/checks?check_run_id=17072241622 plz


in --no-video mode, scrcpy not terminate when disconnected

[v] I have read the FAQ.
[v] I have searched in existing issues.

Environment

OS: Windows
scrcpy version: 2.1.1
installation method: release
device model: google pixel 2 xl, lg wing (and every devices)
Android version: 13

Describe the bug
If scrcpy has video, I can see terminal's process has adb(not showing scrcpy). And it terminates when disconnected so i can start a new one.
But in --no-video , terminal has adb and scrcpy. And only adb terminates when disconnected, scrcpy steel alive and terminal shows it still running, I cannot start new one until I've stop(ctrl+c or kill process in task manager)
I think scrcpy must be terminated too when adb terminated.
[ when ]                     video     video-disconneted      no-video           no-video-disconneted
processes                  adb               -                            adb,scrcpy        scrcpy
can i use console?      no               yes                          no                    no

I forgot images.

Thank you for your report.
Fixed by 0983f0a194db154823842a4728f3c2bb5a3b1cc3.


Update pom.xml

Tyvm!

@mcjp78 There seems to be a problem when compiling on travis. https://travis-ci.org/mwmahlberg/spark-template-thymeleaf/builds/133758993

Ahh, its having an issue casting the capture to an object..
All I did was update the dependencies to support it. Perhaps you can fix it?
Sent from my iPhone
On May 29, 2016, at 11:32 AM, Markus Mahlberg <notifications<EMAIL_ADDRESS>wrote:
@mcjp78https://github.com/mcjp78 There seems to be a problem when compiling on travis. https://travis-ci.org/mwmahlberg/spark-template-thymeleaf/builds/133758993

You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/mwmahlberg/spark-template-thymeleaf/pull/4#issuecomment-222375411, or mute the threadhttps://github.com/notifications/unsubscribe/AMLOco9kFrZysLwgvl1hzM_NzlGj8mgQks5qGduhgaJpZM4IpVjE.

@mcjp78 I have not touched Java for more than a year, so it is probably not the best idea ;) And I am pretty tied into other stuff at the moment. I'd appreciate if you could have a look at it. If you wish, I can hand over the repo or make you a co-admin to improve the workflow.

Ah I see, all right I will see if I can fix it
Sent from my iPhone
On May 30, 2016, at 2:57 AM, Markus Mahlberg <notifications<EMAIL_ADDRESS>wrote:
@mcjp78https://github.com/mcjp78 I have not touched Java for more than a year, so it is probably not the best idea ;) And I am pretty tied into other stuff at the moment. I'd appreciate if you could have a look at it. If you wish, I can hand over the repo or make you a co-admin to improve the workflow.

You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/mwmahlberg/spark-template-thymeleaf/pull/4#issuecomment-222457623, or mute the threadhttps://github.com/notifications/unsubscribe/AMLOcm7OJ6wR1ZXu4dobCZlz0M1qotXvks5qGrRngaJpZM4IpVjE.


Multiple hover play and paused

Hello @Gyanreyer,
Thank you for this library :)
I'm trying to do something but I can't do it with your doc.
I would like to put play and paused each time a link is hovered over a class for example.
But I have the impression that this does not work :
const player = document.querySelector("hover-video-player");

        $(".site-navigation li.page_item").each(function () {
            $(this).on("mouseenter", function () {
                player.playbackState = "play";
            })
            $(this).on("mouseenter", function () {
                player.playbackState = "paused";
            })
        });

I only have this that works:
hover-target=""
But in the end it is not practical if you want to hover over several links. I don't have any additional IDs on my hrefs.
Thanks for your return

Thank you for reaching out, this is a great question! Currently I don't think there's a good supported way to have multiple hover targets for a single hover-video-player instance.
I think it's very reasonable to expect that feature to exist though, so I'll take a look today and see if I can come up with a good solution.

Hello! If you update to v1.1.0, I just added support for multiple hover targets. Based on your example, you should be able to do this now:
<hover-video-player hover-target=".site-navigation li.page_item">
  ...
</hover-video-player>

player.hoverTarget will now also accept iterables of Element instances, so this would also work:
player.hoverTarget = document.querySelectorAll(".site-navigation li.page_item");

Let me know if you have any questions or run into any issues!

Hello @Gyanreyer beautiful ! I'll test this as soon as possible and let you know if it's ok :) Thank you very much !


Expose Raw Public Key Data

We are using ASN1Decoder to parse App Store receipts. As we want to switch from OpenSSL to Security.framework for signature verification, we need access to the raw RSA key data.
We are using SecKeyCreateWithData to instantiate our SecKey. This expects the key in DER format with header. We are prepending the header on the call site, but we do need access to the key data. This PR exposes the raw key data as property.
If this PR gets merged, a DER key - compatible with SecKeyCreateWithData - can be obtained via:
private extension X509PublicKey {

    var rawDERKey: Data? {
        guard let rawKey = self.rawKey else { return nil }

        let header: [UInt8] = [0x30, 0x82, 0x01, 0x22,
                               0x30, 0x0D,
                               0x06, 0x09, 0x2A, 0x86, 0x48, 0x86, 0xF7, 0x0D, 0x01, 0x01, 0x01,
                               0x05, 0x00,
                               0x03, 0x82, 0x01, 0x0F, 0x00]
        var rawDERKey = Data(header)
        rawDERKey.append(rawKey)
        return rawDERKey
    }
}

Update
An unrelated small problem I ran into was:
Git tags in this repo sometimes lack the minor version. (e.g. 1.5 instead of 1.5.0).
The Swift Package manager seems to rely on the minor version and exits with Invalid semantic version string '1.5' when using the following dependency in a package:
.package(url: "https://github.com/filom/ASN1Decoder", from: "1.5")

Your solution to export raw public key don't consider all type of keys and length, but I'm going to add a different way that use existing rawValue and a new DER encoder.
Thanks for the feedback on the package version tag.

Your solution to export raw public key don't consider all type of keys and length

Yes, that's why I didn't include the rawDERKey property in the PR.

but I'm going to add a different way that use existing rawValue and a new DER encoder.

Highly appreciated - Let me know if I can help with anything.
Also thanks for maintaining this library!

I just add a commit and a version 1.6.0
Here an example to create a SecKey:
extension X509PublicKey {

    var secKey: SecKey? {
        guard let publicKeyDerEncoded = derEncodedKey else {
            return nil
        }
        var attributes: [String: Any] = [
            kSecAttrKeyClass as String: kSecAttrKeyClassPublic
        ]
        switch algOid {
        case OID.rsaEncryption.rawValue:
            attributes[kSecAttrKeyType as String] = kSecAttrKeyTypeRSA
        case OID.ecPublicKey.rawValue:
            attributes[kSecAttrKeyType as String] = kSecAttrKeyTypeEC
        default:
            return nil
        }
        var error: Unmanaged<CFError>?
        return SecKeyCreateWithData(publicKeyDerEncoded as CFData, attributes as CFDictionary, &error)
    }
}


Add ClinVar linkout to seqvar details page

Is your feature request related to a problem? Please describe.
We currently do not have a linkout to ClinVar from the seqvar detail page if the variant is not in the local ClinVar copy.
Describe the solution you'd like
Create linkout with canonical SPDI, e.g., NC_000017.11:43045681:T:C. For this, we will need to have a mapping from chromosome name to NCBI sequence identifier+version per release.
The implementation from bihealth/varfish#1223 can be used once completed.
Describe alternatives you've considered
N/A
Additional context

https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh37
https://www.ncbi.nlm.nih.gov/grc/human/data?asm=GRCh38
https://github.com/bihealth/varfish-server/issues/1223

We actually already link to the position in the clinvar card.


ANCOM unit test failures with scipy 0.17.0

The following ANCOM unit tests fail with scipy 0.17.0 on Python 2 and 3:
$ python skbio/stats/tests/test_composition.py
.F.....................F................
======================================================================
FAIL: test_ancom_alternative_test (__main__.AncomTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "skbio/stats/tests/test_composition.py", line 642, in test_ancom_alternative_test
    assert_data_frame_almost_equal(result, exp)
  File "/Users/jairideout/dev/scikit-bio/skbio/util/_testing.py", line 1205, in assert_data_frame_almost_equal
    check_exact=False)
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 1049, in assert_frame_equal
    obj='DataFrame.iloc[:, {0}]'.format(i))
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 946, in assert_series_equal
    check_less_precise, obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 58, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3809)
  File "pandas/src/testing.pyx", line 147, in pandas._testing.assert_almost_equal (pandas/src/testing.c:2685)
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 819, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: DataFrame.iloc[:, 0] are different

DataFrame.iloc[:, 0] values are different (100.0 %)
[left]:  [0, 0, 0, 0, 0, 0, 0]
[right]: [6, 6, 2, 2, 2, 2, 2]

======================================================================
FAIL: test_ancom_normal_data (__main__.AncomTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "skbio/stats/tests/test_composition.py", line 655, in test_ancom_normal_data
    assert_data_frame_almost_equal(result, exp)
  File "/Users/jairideout/dev/scikit-bio/skbio/util/_testing.py", line 1205, in assert_data_frame_almost_equal
    check_exact=False)
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 1049, in assert_frame_equal
    obj='DataFrame.iloc[:, {0}]'.format(i))
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 946, in assert_series_equal
    check_less_precise, obj='{0}'.format(obj))
  File "pandas/src/testing.pyx", line 58, in pandas._testing.assert_almost_equal (pandas/src/testing.c:3809)
  File "pandas/src/testing.pyx", line 147, in pandas._testing.assert_almost_equal (pandas/src/testing.c:2685)
  File "/Users/jairideout/miniconda/envs/scikit-bio/lib/python3.5/site-packages/pandas/util/testing.py", line 819, in raise_assert_detail
    raise AssertionError(msg)
AssertionError: DataFrame.iloc[:, 0] are different

DataFrame.iloc[:, 0] values are different (22.22222 %)
[left]:  [8, 7, 3, 3, 7, 3, 3, 3, 3]
[right]: [8, 8, 3, 3, 8, 3, 3, 3, 3]

----------------------------------------------------------------------
Ran 40 tests in 0.435s

FAILED (failures=2)

The tests pass using the previous scipy release (0.16.1, available via conda and pip). Note that scipy 0.17.0 is currently only available via pip.
The tests are failing because something in scipy.stats.mannwhitneyu changed between scipy 0.16.1 and 0.17.0. Changing test_ancom_alternative_test to pass alternative='less' fixes the test. However, making the same change to test_ancom_normal_data doesn't fix the failure.
See #1258 for original discussion.

Thanks for investigating this.
What do you recommend to fix this?  Can we just update the tests and require the development version of scikit-bio to depend on scipy 0.17.0?

I'm not sure what the fix is -- we'd want to know why the expected values are different between scipy versions before updating the unit tests to use new expected values (the observed vs. expected values are very different).

Of course, let me add some more context
Looking at the test_ancom_normal_data test case
If you look at the original p-value matrix generated by the mann-whitney U-test with scipy==0.16, you get the following.
[[  0.00e+00   5.87e-15   5.48e-15   6.06e-15   5.70e-15   6.10e-15    5.67e-15   4.74e-15   4.08e-15]
 [  5.87e-15   0.00e+00   6.59e-15   6.54e-15   2.40e-01   6.10e-15    6.38e-15   6.28e-15   5.97e-15]
 [  5.48e-15   6.59e-15   0.00e+00   4.46e-01   6.57e-15   1.29e-01    2.06e-01   4.79e-01   2.63e-01]
 [  6.06e-15   6.54e-15   4.46e-01   0.00e+00   6.25e-15   1.99e-01    2.59e-01   3.10e-01   3.65e-01]
 [  5.70e-15   2.40e-01   6.57e-15   6.25e-15   0.00e+00   6.26e-15    6.01e-15   6.15e-15   5.82e-15]
 [  6.10e-15   6.10e-15   1.29e-01   1.99e-01   6.26e-15   0.00e+00    4.44e-01   5.62e-02   3.08e-01]
 [  5.67e-15   6.38e-15   2.06e-01   2.59e-01   6.01e-15   4.44e-01    0.00e+00   1.10e-01   2.91e-01]
 [  4.74e-15   6.28e-15   4.79e-01   3.10e-01   6.15e-15   5.62e-02    1.10e-01   0.00e+00   1.47e-01]
 [  4.08e-15   5.97e-15   2.63e-01   3.65e-01   5.82e-15   3.08e-01    2.91e-01   1.47e-01   0.00e+00]]

Now, if you look at the same p-value matrix with scipy==0.17, you'll get different results
[[  0.00e+00   1.34e-14   1.24e-14   1.28e-14   1.31e-14   1.23e-14    1.30e-14   1.24e-14   1.32e-14]
 [  1.34e-14   0.00e+00   1.34e-14   1.35e-14   6.79e-01   1.32e-14    1.30e-14   1.27e-14   1.35e-14]
 [  1.24e-14   1.34e-14   0.00e+00   6.34e-01   1.32e-14   6.75e-01    2.77e-01   4.24e-01   7.19e-01]
 [  1.28e-14   1.35e-14   6.34e-01   0.00e+00   1.34e-14   5.44e-01    4.49e-01   9.06e-01   9.96e-01]
 [  1.31e-14   6.79e-01   1.32e-14   1.34e-14   0.00e+00   1.28e-14    1.32e-14   1.32e-14   1.33e-14]
 [  1.23e-14   1.32e-14   6.75e-01   5.44e-01   1.28e-14   0.00e+00    3.36e-01   9.84e-01   7.74e-01]
 [  1.30e-14   1.30e-14   2.77e-01   4.49e-01   1.32e-14   3.36e-01    0.00e+00   3.95e-01   2.87e-01]
 [  1.24e-14   1.27e-14   4.24e-01   9.06e-01   1.32e-14   9.84e-01    3.95e-01   0.00e+00   6.47e-01]
 [  1.32e-14   1.35e-14   7.19e-01   9.96e-01   1.33e-14   7.74e-01    2.87e-01   6.47e-01   0.00e+00]]

And this is still different when  alternative='less'
[[  0.00e+00   1.00e+00   6.32e-15   5.91e-15   1.00e+00   6.07e-15   6.13e-15   6.17e-15   6.53e-15]
 [  1.00e+00   0.00e+00   6.38e-15   6.28e-15   4.06e-01   6.61e-15    6.33e-15   6.63e-15   6.28e-15]
 [  6.32e-15   6.38e-15   0.00e+00   2.91e-01   1.00e+00   1.01e-01    4.74e-01   2.10e-01   5.35e-01]
 [  5.91e-15   6.28e-15   2.91e-01   0.00e+00   1.00e+00   3.38e-01    4.02e-01   3.78e-01   5.84e-01]
 [  1.00e+00   4.06e-01   1.00e+00   1.00e+00   0.00e+00   6.55e-15  6.10e-15   6.56e-15   6.80e-15]
 [  6.07e-15   6.61e-15   1.01e-01   3.38e-01   6.55e-15   0.00e+00    8.44e-01   5.16e-01   9.03e-01]
 [  6.13e-15   6.33e-15   4.74e-01   4.02e-01   6.10e-15   8.44e-01     0.00e+00   2.38e-01   7.16e-01]
 [  6.17e-15   6.63e-15   2.10e-01   3.78e-01   6.56e-15   5.16e-01     2.38e-01   0.00e+00   8.21e-01]
 [  6.53e-15   6.28e-15   5.35e-01   5.84e-01   6.80e-15   9.03e-01     7.16e-01   8.21e-01   0.00e+00]]

So, looks like the mann-whitney U-test has completely changed since they incorporated the alternative keyword.  Not sure what the best way to proceed with this.

Thanks for the details! Can these two tests be updated to use a different scipy stat function that is better behaved across scipy versions?

Fixed in #1260.

Hi,
The following two explain what happened with scipy 1.7.0
https://github.com/scipy/scipy/issues/6062
https://github.com/scipy/scipy/pull/6100
The current plan is to revert to the old behavior for 1.7.1, see PR

Thanks @josef-pkt!


Add a license

How is this released and what are the usage options you allow?

I have just added a LICENSE releasing the code to public domain. Code can be used in any way you like.

Thank you, @fln


asset_summary returns empty result when _asset_name is not set

*_asset_policy
_asset_name
docs indicates that _asset_name is optional, however when leaving _asset_name blank result will be empty

Leaving out the _asset_name, you would search for a no-name "" asset under that policy. Does one exist for your policy example?

Yeah it does not, was expecting to get all assets for policy when name is not present.
Dunno can you mark _asset_name just thinking may it cause confusion that missing optional field = search asset with empty name?

I think we just did it to support different ways of specifying no name because they all made sense - sending a request without _asset_name, sending null for _asset_name and specifying an empty string for _asset_name.
Maybe we can add a line somewhere on the API page... For querying bulk assets under a policy we have the /asset_policy_information, but it probably makes sense to add a similar endpoint for asset_summary as there is no way to do that search with just the policy right now.

The absence of asset name should give back royalty (as per CIP-0027 ), the field description was updated in #112 .
As for seperate endpoint for policy across all assets, it's slightly more complicated due to gazillion spammy tokens against a single policy on-chain. Will need to tackle it as seperate architecture (crawler for asset policies), as part of #90 - hence, closing here.


Pinia and Vue Router

Hello. I would like to make your own template by adding pinia and vue router. Can you give me a hand?

Sure, I will create a new branch for this issue, but I'm pretty busy recently and don't have enough time to do this.


feature-request: Grouping tests

I would appreciate if there is a possibility to group tests. So that all test in a group will be run sequentially in a thread. Maybe grouping by folders could be a first approach.
In my case I have tests competing for the backend.

I would also appreciate this feature. I have some tests that also may compete for the backend and would prefer these be run sequentially, while ok to be run in parallel with other tests. Is this in the pipeline?

Has this feature came out yet?


weekly version check 11/8

upgrade k8s to 1.8.3 and 1.7.10
reset etcd back to community tested version of 3.0.17.  Will pull
this into a different PR if requested

ETCD_SHA256 is wrong. Should be 274c46a7f8d26f7ae99d6880610f54933cbcf7f3beafa19236c52eb5df8c7a0b


POST /login route not exists in the route:list

I cannot submit a POST request on the LoginController which handles the LoginProxy because it does not exists in the route:list
This is the return of my php artisan route:list
|        | GET|HEAD | oauth/personal-access-tokens            |      | \Laravel\Passport\Http\Controllers\PersonalAccessTokenController@forUser   | web,auth   | |        | POST     | oauth/personal-access-tokens            |      | \Laravel\Passport\Http\Controllers\PersonalAccessTokenController@store     | web,auth   | |        | DELETE   | oauth/personal-access-tokens/{token_id} |      | \Laravel\Passport\Http\Controllers\PersonalAccessTokenController@destroy   | web,auth   | |        | GET|HEAD | oauth/scopes                            |      | \Laravel\Passport\Http\Controllers\ScopeController@all                     | web,auth   | |        | POST     | oauth/token                             |      | \Laravel\Passport\Http\Controllers\AccessTokenController@issueToken        | throttle   | |        | POST     | oauth/token/refresh                     |      | \Laravel\Passport\Http\Controllers\TransientTokenController@refresh        | web,auth   | |        | GET|HEAD | oauth/tokens                            |      | \Laravel\Passport\Http\Controllers\AuthorizedAccessTokenController@forUser | web,auth   | |        | DELETE   | oauth/tokens/{token_id}                 |      | \Laravel\Passport\Http\Controllers\AuthorizedAccessTokenController@destroy | web,auth   |

As far as I can see it's there
Check https://github.com/esbenp/larapi/blob/master/infrastructure/Auth/routes_public.php#L3
Here is a screenshot of my case (I have one or a couple of my own routes added for tests)

@geraldarcega  You are probably missing Infrastructure\Http\RouteServiceProvider::class  in the providers arrray ( inside   config/app.php

Closed due to inactivity.


remove extra logic, now present in the base class

This update removes the extra logic which should now be handled correctly in the base class.
Note: Since I don't have a test environment for this tap myself, please do test this locally to ensure all is still working as expected.

@jtimeus-slalom - I believe the fixed version (here should do the trick now without this extra code.


Document Collaborate with Us page

Overview
Document file and code structure for Collaborate with Us page
Action Items

[ ] Document file and code structure for Collaborate with Us page

Resources/Instructions
Civic Tech Index Site Architecture documentation can be updated here

@bhaggya has completed core documentation.  Future changes are possible as page functionality is updated.


Could you please provide:

Your input code
The output you get
What would you expect instead.

Sorry, I don't understand the problem.
Could you please provide:

Your input code
The output you get
What would you expect instead.

I guess this might be the same as issue #50
Closing this.

I guess this might be the same as issue #50
Closing this.


Scene dynamic initial

Version

react-native-router-flux v3.26.13
react-native v0.26.3

Expected behaviour
  let isLoggedIn = this.state.isLoggedIn;

   <Scene
      key="login" component={Login} title="Login" type="reset" hideNavBar
      initial={isLoggedIn}
    />
    <Scene
      key="main" tabs default="Dashboard" tabBarStyle={colorStyles.appBg}
      initial={isLoggedIn}
    >

I hope initial is dynamic
Dynamic Routing(3.x release) allows you to choose which scene to render depending on application state , But  Switch should be used together with tabs={true} property.

Scene is not real component (it doesn't render nothing), so you can't use it as Component replacements. You could use it only inside Router.

Also, even inside a router you should have have state, as you should not re-render the whole app. And given that any "isLoggedIn" will be async, you should be routing to another component after determining a logged in state.

@cridenour  how should this be achieved then?
scenes/index.js
export default Actions.create(
  <Scene
    key="root"
  >
    {Scene}
    {OtherScene}
    { /* ... more Scenes */}
  </Scene>,
);

root.js
export default function Root() {
  return (
    <Provider store={store}>
      <RouterWithRedux scenes={scenes} />
    </Provider>
  );
}

How should I switch between Scene and OtherScene depending on the state?
Should I make Root a Stateful Component and handle on component render, dispatching Actions.key?
I'm very confused and this has been taking me a lot of time to figure it out correctly.
Thanks in advance.

@wachunei any update on how you handled this?

@mbenjamin618  I've created an initial Scene (SplashScreenScene here) which has set an SplashScreen component that handles storage and rehydration and then redirects to corresponding scene.


Default value for ARG $BASE_IMAGE results in empty or invalid base image name

I'm sorry @Tpuljak but I have another one :D
When I try to deploy this repo https://github.com/johnnypea/devcontainer-php I'm getting
 devcontainer-php |  1 warning found (use docker --debug to expand):
 devcontainer-php |  - InvalidDefaultArgInFrom: Default value for ARG $BASE_IMAGE results in empty or invalid base image name (line 4)
 devcontainer-php | [4266 ms] Start: Run: docker compose --project-name devcontainer-php-qu3q2n0a -f /tmp/overrides/daytona-compose-override.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.build-1732635240144.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.containerFeatures-1732635241857-0d973171-3487-49b6-89f9-919ada68c752.yml up -d
 devcontainer-php | WARN[0000] a network with name devcontainer_default exists but was not created for project "devcontainer-php-qu3q2n0a".
 devcontainer-php | Set `external: true` to use an existing network
 devcontainer-php | [+] Running 0/1
 devcontainer-php |  ⠙ Container devcontainer-php-qu3q2n0a-php-unit-1  Starting0.2s
 devcontainer-php | Error: Command failed: docker compose --project-name devcontainer-php-qu3q2n0a -f /tmp/overrides/daytona-compose-override.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.build-1732635240144.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.containerFeatures-1732635241857-0d973171-3487-49b6-89f9-919ada68c752.yml up -d
 devcontainer-php |     at ftA (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:430:3355)
 devcontainer-php |     at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
 devcontainer-php |     at async htA (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:410:3496)
 devcontainer-php |     at async TtA (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:482:4021)
 devcontainer-php |     at async iB (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:482:4963)
 devcontainer-php |     at async wrA (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:663:203)
 devcontainer-php |     at async DrA (/usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:662:14830)
 devcontainer-php |     at async /usr/local/share/nvm/versions/node/v20.17.0/lib/node_modules/@devcontainers/cli/dist/spec-node/devContainersSpecCLI.js:482:1190
 devcontainer-php | {"outcome":"error","message":"Command failed: docker compose --project-name devcontainer-php-qu3q2n0a -f /tmp/overrides/daytona-compose-override.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.build-1732635240144.yml -f /tmp/devcontainercli-daytona/docker-compose/docker-compose.devcontainer.containerFeatures-1732635241857-0d973171-3487-49b6-89f9-919ada68c752.yml up -d","description":"An error occurred starting Docker Compose up."}
FATA[0016] failed to create workspace: container exited with status 1

Okay, this was a bit hectic to debug 😅 .
First of all, the  InvalidDefaultArgInFrom: Default value for ARG $BASE_IMAGE results in empty or invalid base image name (line 4) warning is not important. It's just Docker's warning related to https://github.com/devcontainers/cli/blob/main/scripts/updateUID.Dockerfile. Not much we can do there but it's just a warning, not the cause of the issue.
The actual issue is regarding permissions inside the container.

This is the screenshot of the docker logs of that container produced by the entrypoint. As you can see, the nginx conf can not be set due to a permissions issue.
This isn't an issue when running the devcontainer using vscode, but only on accident. It's not an issue because the UID/GID doesn't get remapped.
I tried to run the devcontainer on a different user and the same thing happens as it does in daytona. I did the following:

docker run --privileged daytonaio/workspace-project
docker exec INTO THE CONTAINER
sudo useradd -m toma
sudo usermod -a -G docker toma
sudo su toma
cd ~ && git clone https://github.com/johnnypea/devcontainer-php.git && cd devcontainer-php
devcontainer up --workspace-folder . --log-level=trace

This results in the same error as in Daytona:

Maybe you can try to set the ownership of /etc/nginx to www-data inside the Dockerfile.
I'll close this issue here since it's not related to Daytona directly but feel free to continue the discussion below.

@Tpuljak thank you for looking into this. I set UID (1000) and GID (1000) but now I'm getting this:
 WORKSPACE        | ✓ Workspace creation complete. Pending start...
 WORKSPACE        | ✓ Starting workspace
 devcontainer-php | Starting project devcontainer-php
 devcontainer-php | Reading devcontainer configuration...
 devcontainer-php | Running devcontainer user commands...
 devcontainer-php | [2 ms] @devcontainers/cli 0.72.0. Node.js v20.17.0. linux 6.8.0-45-generic x64.
 devcontainer-php | {"outcome":"success","result":"done"}
 devcontainer-php | [2 ms] @devcontainers/cli 0.72.0. Node.js v20.17.0. linux 6.8.0-45-generic x64.
 devcontainer-php | [276 ms] Start: Run: docker compose -f /tmp/overrides/daytona-compose-override.yml --profile * config
 devcontainer-php | {"outcome":"success","containerId":"f3dfc57dc806f4b8ad81f9893eefbcd2d80b37ea06070d307623eb5eb76db654","composeProjectName":"devcontainer-php-recwy5m0qms8","remoteUser":"www-data","remoteWorkspaceFolder":"/var/www/html"}
 devcontainer-php | bash: line 1: sudo: command not found
FATA[0024] failed to create workspace: bash: line 1: sudo: command not found

How can I debug this? Or where can I find more verbose logs?

@johnnypea I believe this fails now when Daytona attempts to install the agent inside the container. sudo is a requirement here. Can you please try again when adding sudo into the image?

@Tpuljak ok, I got pass that but... https://github.com/johnnypea/devcontainer-php
 Opening the workspace in VS Code ...

Setting up IDE customizations...
FATA[0057] json: cannot unmarshal object into Go value of type []devcontainer.Configuration

VS Code opens up and it seems like I can interact with the workspace.


You will need to set allow_dangerous_deserialization to True

Example 10_RAG_for_HTML_docs_with_Langchain_NVIDIA_AI_Endpoints fails with error:
ValueError: The de-serialization relies loading a pickle file. Pickle files can be modified to deliver a malicious payload that results in execution of arbitrary code on your machine.You will need to set allow_dangerous_deserialization to True to enable deserialization. If you do this, make sure that you trust the source of the data. For example, if you are loading a file that you created, and no that no one else has modified the file, then this is safe to do. Do not set this to True if you are loading a file from an untrusted source (e.g., some random site on the internet.).

Thank you for noticing this.
We have fixed this.
https://github.com/NVIDIA/GenerativeAIExamples/blob/main/RAG/notebooks/langchain/RAG_for_HTML_docs_with_Langchain_NVIDIA_AI_Endpoints.ipynb