Excessive commemoration in Blessed Trinity Sunday

For the feast of the Blessed Trinity 2022 the commemoration of the 1st Sunday after Pentecost is included. This is against 1962 rubrics as indicated in the 1962 Missale Romanum - and verified on the SSPX Ordo (https://1962ordo.today/day/trinity-sunday-2-2-2-2/)

Fixed in #127


State of Project and .Net5.0 support

Hey,
As a Preamble I want to clarify that well aware of the huge amount of time it takes to maintain a large open source project and that this for (most of us) all done in our Freetime and nobody has any rights or otherwise to pressure you (author, maintainers) to do anything on the project.
But, I followed this project some time now and I wonder if the current Maintainers are still willing to support this project. There are a large number of open issues and the documentation is very outdated (having still references to codeplex while codeplex will shutdown completely in 3 months).
I would kindly know if the current maintains are able/willing to continue support this project. Is there any "roadmap" to implement support for the ongoing tech stack?

I've just discovered this project, and was quite excited to find it, because it looks like it could be a great alternative to the ancient WPF WebBroswer control. That is until I saw the large number of open issues and pull requests from quite some time ago.
So I'd also like to know if this project will be maintained going forward before  invest time into integrating it into my project(s).
Thanks!

@JPVenson You can find the documentation here
There should be all links fixed, but i agree, the README.md has still references to codeplex.
Also keep in mind (as @yannduran mentioned) that the readme clearly states, for over 5 years now, that Arthur is looking for contributors/maintainers that are willingly to take over as he is unable to maintain it.


Link

How can I change text message or link that have been sended through sms

I am having a problem with that too. I dont know what i am using wrong or what i am supposed to do at the point.

are you both fuxking retarded?

No But I am a noob. Why would not knowing a language and code make u below 3rd grade lvl.

are you both fuxking retarded?

I'm zero -5 is my level 🤧🥲


ConnectionError: Playwright process has been terminated with code

Describe the bug
Recently I've started getting a lot of errors where my browser hangs for a while and after any interaction with browser ends with error  "ConnectionError: Playwright process has been terminated with code".  Happens in Gitlab and on local Windows machine. Appears in  random parts of different test cases so I do not have steps to reproduce, but maybe you could spot some bug based on robot and playwright logs.
In recent run on local machine flow was the following:

It's started with error in Wait For Elements State keyword.

playwright:
2023-06-15T08:51:27.538Z pw:api => locator.waitFor started
2023-06-15T08:51:27.538Z pw:api waiting for locator('*****************************************************************') to be visible
2023-06-15T08:51:47.537Z pw:api <= locator.waitFor failed
{"level":30,"time":"2023-06-15T08:51:47.537Z","pid":12912,"hostname":"************","msg":"Error of node method  waitForElementState"}
================= Original suppressed error =================
locator.waitFor: Timeout 20000ms exceeded.
=========================== logs ===========================
waiting for locator('*****************************************************************') to be visible
============================================================
    at waitForElementState (C:\Users\********\Docs\code\*********\.venv\lib\site-packages\Browser\wrapper\index.js:8477:19)
    at async PlaywrightServer.waitForElementsState (C:\Users\********\Docs\code\*********\.venv\lib\site-packages\Browser\wrapper\index.js:9987:28) {
  name: 'TimeoutError'
}
=============================================================

robot:
Arguments: [ '*****************************************************************' ]
TimeoutError: locator.waitFor: Timeout 20000ms exceeded.
=========================== logs ===========================
waiting for locator('*****************************************************************') to be visible
============================================================
Tip: Use "Set Browser Timeout" for increasing the timeout or double check your locator as the targeted element(s) couldn't be found.
10:51:47.554 	DEBUG 	Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 160, in grpc_channel
    yield playwright_pb2_grpc.PlaywrightStub(self._channel)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\waiter.py", line 140, in _wait_for_elements_state
    response = stub.WaitForElementsState(
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 1030, in __call__
    return _end_unary_response_blocking(state, call, False, None)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 910, in _end_unary_response_blocking
    raise _InactiveRpcError(state)  # pytype: disable=not-instantiable
grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
	status = StatusCode.DEADLINE_EXCEEDED
	details = "TimeoutError: locator.waitFor: Timeout 20000ms exceeded.
=========================== logs ===========================
waiting for locator('*****************************************************************') to be visible
============================================================"
	debug_error_string = "UNKNOWN:Error received from peer  {created_time:"2023-06-15T08:51:47.556360349+00:00", grpc_status:4, grpc_message:"TimeoutError: locator.waitFor: Timeout 20000ms exceeded.\n=========================== logs ===========================\nwaiting for locator(\'*****************************************************************\') to be visible\n============================================================"}"
>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1122, in run_keyword
    raise e
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1111, in run_keyword
    return DynamicCore.run_keyword(self, name, args, kwargs)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\robotlibcore.py", line 122, in run_keyword
    return self.keywords[name](*args, **(kwargs or {}))
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\waiter.py", line 102, in wait_for_elements_state
    return self._wait_for_elements_state(
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\waiter.py", line 145, in _wait_for_elements_state
    logger.info(response.log)
  File "C:\Users\********\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 164, in grpc_channel
    raise AssertionError(error.details())
AssertionError: TimeoutError: locator.waitFor: Timeout 20000ms exceeded.
=========================== logs ===========================
waiting for locator('*****************************************************************') to be visible
============================================================
Tip: Use "Set Browser Timeout" for increasing the timeout or double check your locator as the targeted element(s) couldn't be found.

In teardown I try to make screenshot if test failed and than close page and context (I login in suite setup, save storage state and  reuse it to create new context and page in test setup)

playwright:
2023-06-15T08:51:47.557Z pw:api => page.screenshot started
2023-06-15T08:51:47.558Z pw:api taking page screenshot
2023-06-15T08:52:07.561Z pw:api <= page.screenshot failed
{"level":30,"time":"2023-06-15T08:52:07.562Z","pid":12912,"hostname":"************","msg":"Error of node method  takeScreenshot"}
================= Original suppressed error =================
page.screenshot: Timeout 20000ms exceeded.
=========================== logs ===========================
taking page screenshot
============================================================
    at takeScreenshot (C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\wrapper\index.js:8324:16)
    at PlaywrightServer.takeScreenshot (C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\wrapper\index.js:9987:34)
    at C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\wrapper\node_modules\@grpc\grpc-js\build\src\server.js:821:17
    at Http2ServerCallStream.safeDeserializeMessage (C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\wrapper\node_modules\@grpc\grpc-js\build\src\server-call.js:395:13)
    at ServerHttp2Stream.onEnd (C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\wrapper\node_modules\@grpc\grpc-js\build\src\server-call.js:382:22) {
  name: 'TimeoutError'
}
=============================================================

robot - Screenshot:
Arguments: [ 'C:\\Users\\********\\Docs\\code\\e2e-tests\\src\\variables\\..\\..\\artifacts\\screenshots\\browser-screenshot-{index}' | fullPage=True ]
Return: None
TimeoutError: page.screenshot: Timeout 20000ms exceeded.
=========================== logs ===========================
taking page screenshot
============================================================
Tip: Use "Set Browser Timeout" for increasing the timeout or double check your locator as the targeted element(s) couldn't be found.
10:52:07.580 	DEBUG 	Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 160, in grpc_channel
    yield playwright_pb2_grpc.PlaywrightStub(self._channel)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\browser_control.py", line 185, in take_screenshot
    response = stub.TakeScreenshot(
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 1030, in __call__
    return _end_unary_response_blocking(state, call, False, None)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 910, in _end_unary_response_blocking
    raise _InactiveRpcError(state)  # pytype: disable=not-instantiable
grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
	status = StatusCode.DEADLINE_EXCEEDED
	details = "TimeoutError: page.screenshot: Timeout 20000ms exceeded.
=========================== logs ===========================
taking page screenshot
============================================================"
	debug_error_string = "UNKNOWN:Error received from peer  {created_time:"2023-06-15T08:52:07.57355539+00:00", grpc_status:4, grpc_message:"TimeoutError: page.screenshot: Timeout 20000ms exceeded.\n=========================== logs ===========================\ntaking page screenshot\n============================================================"}"
>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1122, in run_keyword
    raise e
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1111, in run_keyword
    return DynamicCore.run_keyword(self, name, args, kwargs)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\robotlibcore.py", line 122, in run_keyword
    return self.keywords[name](*args, **(kwargs or {}))
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\browser_control.py", line 220, in take_screenshot
    return None
  File "C:\Users\********\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 164, in grpc_channel
    raise AssertionError(error.details())
AssertionError: TimeoutError: page.screenshot: Timeout 20000ms exceeded.
=========================== logs ===========================
taking page screenshot
============================================================
Tip: Use "Set Browser Timeout" for increasing the timeout or double check your locator as the targeted element(s) couldn't be found.

robot - Close Page:
10:52:07.587 	TRACE 	Arguments: [  ]
10:52:07.925 	INFO 	[
  {
    "type": "firefox",
    "id": "browser=1e6c408f-907b-45f1-ac2c-08bbf9e32f9a",
    "contexts": [
      {
        "type": "context",
        "id": "context=ca283bd7-8b46-478a-8841-e33e0e3032be",
        "activePage": "page=405f816d-e4fe-4c7e-957e-03c1971695b5",
        "pages": [
          {
            "type": "page",
            "title": null,
            "url": "*****************************************",
            "id": "page=405f816d-e4fe-4c7e-957e-03c1971695b5",
            "timestamp":<PHONE_NUMBER>.008
          }
        ]
      }
    ],
    "activeContext": "context=ca283bd7-8b46-478a-8841-e33e0e3032be",
    "activeBrowser": true
  }
]
10:52:07.925 	INFO 	Switching browser to CURRENT
10:52:07.941 	INFO 	Active context id
10:52:07.941 	INFO 	Switching browser to browser=1e6c408f-907b-45f1-ac2c-08bbf9e32f9a
10:52:07.941 	INFO 	Successfully changed active browser
10:52:07.941 	INFO 	Switching context to CURRENT in CURRENT
10:52:07.941 	INFO 	Returned active context id
10:52:07.941 	INFO 	Switching context to context=ca283bd7-8b46-478a-8841-e33e0e3032be in CURRENT
10:52:08.288 	INFO 	[
  {
    "type": "firefox",
    "id": "browser=1e6c408f-907b-45f1-ac2c-08bbf9e32f9a",
    "contexts": [
      {
        "type": "context",
        "id": "context=ca283bd7-8b46-478a-8841-e33e0e3032be",
        "activePage": "page=405f816d-e4fe-4c7e-957e-03c1971695b5",
        "pages": [
          {
            "type": "page",
            "title": null,
            "url": "*************************************************",
            "id": "page=405f816d-e4fe-4c7e-957e-03c1971695b5",
            "timestamp":<PHONE_NUMBER>.008
          }
        ]
      }
    ],
    "activeContext": "context=ca283bd7-8b46-478a-8841-e33e0e3032be",
    "activeBrowser": true
  }
]
10:52:08.318 	INFO 	Successfully changed active context
10:52:21.365 	TRACE 	Return: None
10:52:21.365 	FAIL 	Stream removed
10:52:21.385 	DEBUG 	Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 160, in grpc_channel
    yield playwright_pb2_grpc.PlaywrightStub(self._channel)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\playwright_state.py", line 283, in close_page
    response = stub.ClosePage(Request().Empty())
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 1030, in __call__
    return _end_unary_response_blocking(state, call, False, None)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\grpc\_channel.py", line 910, in _end_unary_response_blocking
    raise _InactiveRpcError(state)  # pytype: disable=not-instantiable
grpc._channel._InactiveRpcError: <_InactiveRpcError of RPC that terminated with:
	status = StatusCode.UNKNOWN
	details = "Stream removed"
	debug_error_string = "UNKNOWN:Error received from peer  {created_time:"2023-06-15T08:52:21.37488401+00:00", grpc_status:2, grpc_message:"Stream removed"}"
>

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1122, in run_keyword
    raise e
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1111, in run_keyword
    return DynamicCore.run_keyword(self, name, args, kwargs)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\robotlibcore.py", line 122, in run_keyword
    return self.keywords[name](*args, **(kwargs or {}))
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\playwright_state.py", line 286, in close_page
    result.append(
  File "C:\Users\********\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 137, in __exit__
    self.gen.throw(typ, value, traceback)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 164, in grpc_channel
    raise AssertionError(error.details())
AssertionError: Stream removed

robot - Close Context:
10:52:21.385 	TRACE 	Arguments: [  ]
10:52:23.440 	TRACE 	Return: None
10:52:23.440 	FAIL 	ConnectionError: Playwright process has been terminated with code<PHONE_NUMBER>
10:52:23.440 	DEBUG 	Traceback (most recent call last):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\browser.py", line 1111, in run_keyword
    return DynamicCore.run_keyword(self, name, args, kwargs)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\robotlibcore.py", line 122, in run_keyword
    return self.keywords[name](*args, **(kwargs or {}))
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\playwright_state.py", line 181, in close_context
    for browser_instance in self._get_browser_ids(browser):
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\playwright_state.py", line 210, in _get_browser_ids
    catalog = self.get_browser_catalog()
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\assertion_engine.py", line 55, in with_assertion_polling
    return wrapped(*args, **kwargs)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\keywords\playwright_state.py", line 977, in get_browser_catalog
    with self.playwright.grpc_channel() as stub:
  File "C:\Users\********\AppData\Local\Programs\Python\Python39\lib\contextlib.py", line 119, in __enter__
    return next(self.gen)
  File "C:\Users\********\Docs\code\e2e-tests\.venv\lib\site-packages\Browser\playwright.py", line 154, in grpc_channel
    raise ConnectionError(
ConnectionError: Playwright process has been terminated with code<PHONE_NUMBER>

After that any attempt to create new context ends with error ConnectionError: Playwright process has been terminated with code.
Additionally at the very end of playwright log there is:

#
# Fatal error in , line 0
# Fatal JavaScript invalid size error 169220804
#
#
#
#FailureMessage Object: 0000009A2F1FE310
 1: 00007FF6362DD51F node_api_throw_syntax_error+175743
 2: 00007FF6361F37BF v8::CTypeInfoBuilder<void>::Build+12703
 3: 00007FF63709D852 V8_Fatal+162
 4: 00007FF636BAAB05 v8::internal::FactoryBase<v8::internal::Factory>::NewFixedArray+101
 5: 00007FF636A4EE2E v8::Message::GetIsolate+16478
 6: 00007FF63689AE10 v8::internal::CompilationCache::IsEnabledScriptAndEval+25952
 7: 00007FF636DA8051 v8::internal::SetupIsolateDelegate::SetupHeap+558193
 8: 00007FF5C1D6F5DC

Versions:
robotframework-browser 16.2.0
robotframework 5.0.1
node v18.16.0

@allcontributors please add @JaPyR for bugs

Have you tried:
Wait For Condition    Element States    ${locator}    Contains    attached

Maybe it is just time to remove that keyword.

Looks like I did not mention quite important thing that it was happening in Firefox. After switching to Chromium problem disappeared.

Maybe it is just time to remove that keyword.

If it's internal implementation is different than Wait For Condition maybe it's better to switch it internally, but leave the keyword. Such keyword could be quite popular in tests and removing it will require changes in a lot of places.

Ok, we found the problem at our end last week, it was completely unrelated after all, just coincidence (what are the odds it failed at the exact same keyword with exactly the same message).
The actual problem in our case was the disk image running out of space (and crashing playwright), since it gets rebuild every time, it failed at exactly the same step (during the Wait For Element keyword), and the error happened to be exactly the same as described in this ticket. A few successful runs on Friday and this weekend seem to prove that the disk image size was the actual issue at our end.

I think we can close this issue.


RigidBody2D is missing set_collision_layer func

Operating system or device - Godot version:
2.1
I'm messing around with rigid bodies with 2d platforming and collision layers/masks. Looks like calling:
rigidbody.set_collision_layer(0)
returns
Invalid call. Nonexistent function 'set_collision_layer' in base 'RigidBody2D (player.gd)'.
Collision layer does work for RigidBody2D as well because if you change it from the inspector, it works as intended :D

Eh. I'm dumb:
https://github.com/godotengine/godot/blob/c05ff0577fd9cc39a6968e65743f7d7da711bfe2/scene/2d/physics_body_2d.cpp#L111
It's set_layer_mask


Support customizing colors for rows in DataTable

Description
Add argument color to DataRow to support customizing colors in DataTable. This will enable users to modify the colors when a row is selected, enabled, disabled, hovered, focused and pressed. It can also allow users to for example have alternate colors per row which was the feature request in the issue.
This is part of a larger change to update the DataTable, to support theming and bring it up to Material specifications.
See example:

Related Issues
Related issues:
https://github.com/flutter/flutter/issues/56079
https://github.com/flutter/flutter/issues/21864
Tests
I added the following tests:

DataRow renders custom colors when pressed
DataRow renders custom colors when selected
DataRow renders custom colors when disabled

Checklist
Before you create this PR confirm that it meets all requirements listed below by checking the relevant checkboxes ([x]). This will ensure a smooth and quick review process.

[X] I read the Contributor Guide and followed the process outlined there for submitting PRs.
[X] I signed the CLA.
[X] I read and followed the Flutter Style Guide, including Features we expect every widget to implement.
[X] I read the Tree Hygiene wiki page, which explains my responsibilities.
[X] I updated/added relevant documentation (doc comments with ///).
[X] All existing and new tests are passing.
[X] The analyzer (flutter analyze --flutter-repo) does not report any problems on my PR.
[X] I am willing to follow-up on review comments in a timely manner.

Breaking Change
Did any tests fail when you ran them? Please read Handling breaking changes.

[X] No, no existing tests failed, so this is not a breaking change.
[ ] Yes, this is a breaking change. If not, delete the remainder of this section.

[ ] I wrote a design doc: https://flutter.dev/go/template Replace this with a link to your design doc's short link
[ ] I got input from the developer relations team, specifically from: Replace with the names of who gave advice
[ ] I wrote a migration guide: https://flutter.dev/go/breaking-changes-template Replace this with a link to a pull request that adds the migration guide to https://flutter.dev/docs/release/breaking-changes

@HansMuller is it possible to have this on beta-channel? Or what are the procedures to have these changes approved for beta?

Why does this want a MaterialColor and not a plain Color? Are you doing something with the entire swatch that's included in a MaterialColor?

It's a MaterialStateProperty<Color> because it's useful to be able to specify different colors for different states (or combinations of states).

No, I totally understand the utility of providing different colors for different states. I was just using this last night and found that I got runtime (not compile time) errors when I provided a MaterialStateProperty<Color> and was able to fix them by changing to MaterialStateProperty<MaterialColor>. This is with a web project, Flutter version Flutter (Channel beta, 1.20.0-7.4.pre, on Mac OS X 10.15.6 19G73, locale en-US).

That shouldn't be necessary. Please file an issue with an example that demos the problem and we'll investigate.

Well, now I can't reproduce it, so it must have been a stale build cache somehow messing me up.


Scatter plot from xarray dataset fails with dynamic=False

I'm been trying to save a simple scatter plot as a html file and with a really basic example (variable vs time) it works fine but when trying to plot variables against each other, dynamic=False stops it working.
I've tested this on an xarray test dataset so it's reproducible.
import xarray as xr
import hvplot
import hvplot.pandas
import hvplot.xarray
import geoviews as gv
import cartopy.crs as ccrs
import holoviews as hv
from holoviews import opts

air_ds = xr.tutorial.open_dataset('air_temperature').load()

<xarray.Dataset>
Dimensions:  (lat: 25, lon: 53, time: 2920)
Coordinates:
  * lat      (lat) float32 75.0 72.5 70.0 67.5 65.0 ... 25.0 22.5 20.0 17.5 15.0
  * lon      (lon) float32 200.0 202.5 205.0 207.5 ... 322.5 325.0 327.5 330.0
  * time     (time) datetime64[ns] 2013-01-01 ... 2014-12-31T18:00:00
Data variables:
    air      (time, lat, lon) float32 241.2 242.5 243.5 ... 296.49 296.19 295.69

This works perfectly:
scat = air_ds.isel(lat=0).isel(time=slice(0,10), lon=slice(0,10)).hvplot.scatter(x='time', y='air', groupby='lon', height=600, width=600, dynamic=False)
and I can either display it or save it to a HTML file
hvplot.show(scat)
hv.save(scat, 'graph.html')
However, if instead of trying to plot a scatter of a variable against a coordinate (e.g. time), I try to plot two variables against each other then I run into problems.
This works as expected still:
#create second variable based on first
air_ds['air2'] = air_ds.air + 2

#cut a smaller slice out of the dataset as don't need it to be huge to demonstrate issue
scat = air_ds.isel(lat=0).isel(time=slice(0,10), lon=slice(0,10)).hvplot.scatter(x='air2', y='air', groupby='lon', height=600, width=600)

hvplot.show(scat) #this works and shows the scatter plot with slider fine

but adding in dynamic=False then causes it to stop working:
scat = air_ds.isel(lat=0).isel(time=slice(0,10), lon=slice(0,10)).hvplot.scatter(x='air2', y='air', groupby='lon', height=600, width=600, dynamic=False)

hvplot.show(scat) #this doesn't show the plot, it's blank except for the slider

DataFrames don't seem to have the same issue and this work fine.
df = air_ds.to_dataframe()
scat = df.hvplot.scatter(x='air2', y='air', groupby='lon', height=600, width=600, dynamic=False)
hv.save(scat, 'temp.html')

I'd say this is a work-around for now but not a solution.

@philippjfr is this definitely a bug then? I wasn't sure if I was doing something wrong. If it's a bug I'll stop trying to get it to work :-)

The problem here appears to be something to do with the size of the plot, if you increase it to width=900 height=900 it all works.


Any way to cut a quarter of the circle?

I want a slice of pizza.
Tried to wrap the <RadialGradient/> with a <View style={{height: radius/2, width/2}}/>, but the gradient will draw outside it anyway.
Is it possible?

Fixed with <View style={{height: radius/2, width/2, overflow: 'hidden' }}/> hehe


Add new medium salvage

Media

Changelog
:cl:

add: Added a new medium salvage to rotation.

Tests pass locally, not really sure what's up.

Seems like yet another test runner issue.


Remove Database from Model

Type of PR:

[ ] Bugfix
[ ] Feature
[x] Refactor
[ ] Code style update
[ ] Build-related changes
[ ] Test
[ ] Documentation
[ ] Other, please describe:

Breaking changes:

[ ] No
[x] Yes

The following attributes have been removed from the Model:

_database

The following methods have been removed from the Model:

$database
$setDatabase
$query
$delete
$deleteByKeyName
$deleteByCompositeKeyName

Details
Purpose
The purpose of this PR is to remove Database access from the Model in order to simplify the Model and enforce a repository pattern when using the ORM. This means that we will stop relying on the Model to retrieve another Model and instead use the Repository or Database to fetch any other models.
Changes

Removed Database from Model & any other associated methods
Removed tests that tie back to the removed logic

AWESOOOME! Thanks a lot. Let's merge this after we make a new release for MorphOne and withAll and withAllRecursive methods. Since this is a breaking change, I think it's better to push plain new feature release first 👍

Thanks!!!!! 🙌  🎉


[util] clangd complaining about unknown argument '-fno-canonical-system-headers'

I see this on the first line of .c sources, but I'm not exactly sure why.
I have a sneaking suspicion that compile_commands.json is using the wrong gcc, but I'm not sure how that would work; the bazel aquery results explicitly call /usr/bin/gcc.
@drewmacrae IIRC, you mentioned something about "gcc" being a lie for host-targeted builds. Could you point me to where that misdirection occurs?
The error:
Unknown argument: '-fno-canonical-system-headers' [drv_unknown_argument]

https://github.com/lowRISC/bazel-embedded/tree/riscv32/toolchains/lowrisc_toolchain_rv32imc/clang_wrappers There's a set of symlinks in here

Oh, I think I got it backwards! It looks like this only affects cross-compiles for riscv — I'm guessing executing gcc causes clang_wrappers/gcc to run, which just execs the riscv clang binary.

@a-will @cfrantz @timothytrippel @mundaym is this still relevant?


Prevent DB query when value is empty

This was raised in #3835
We were doing one extra query even when there is no value. The change to strict comparison over loose was made to allow the use of 0 keys.
This keeps the strict comparison but check if the value is not empty before attempting to make any query.
EDIT: from user feedback this solves the problem and works as expected.

A new inspection was created.

The inspection completed: No new issues

A new inspection was created.

The inspection completed: No new issues

Guys - I don't get it. Is this ready to merge? 👀

A new inspection was created.

Hello @tabacitu
Now is ready, after @promatik confirmed the changes are good I added them to fetch_and_create and relationship_select too!

The inspection completed: No new issues


Fix: failed transactions are displayed as successful in Activity tab

Closes #2252, closes #2238

Before PR
After PR

@vladyslav-iosdev bump :)

@hboon what do i need to check here?

@vladyslav-iosdev compare the screenshots to check if it matches the title/body of the PR, as well as the code that was modified.

@hboon not it seems like ok. Updated titles with appropriate values

@vladyslav-iosdev approve it and merge then :)


Convo List Performance

Outputs
Loaded 2015 conversations in 17.609s
Second time loaded 2015 conversations in 0.197s
Loaded 2015 conversations in 0.326s
Second time loaded 2015 conversations in 0.192s

Turned out to just be an iOS bug.


ENTMQBR-1822 Jon Plugin Configuration doc and start/stop functions

Added start/stop/restart of the broker process.

@andytaylor Andy can you review this? thx.


fix(textarea): update disabled text color

fixes #165
PR Checklist
Please check if your PR fulfills the following requirements:

[ ] Tests for the changes have been added (for bug fixes / features)
[ ] Docs have been added / updated (for bug fixes / features)
[ ] If applicable, have a visual design approval

PR Type
What kind of change does this PR introduce?

[x] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] CI related changes
[ ] Documentation content changes
[ ] clarity.design website / infrastructure changes
[ ] Other... Please describe:

What is the current behavior?
The text color in a disabled textarea didn't match the color of other disabled elements
Issue Number: #165
What is the new behavior?
The color now matches the color of other disabled inputs

Does this PR introduce a breaking change?

[ ] Yes
[x] No

Other information

The color contrast of this doesn't pass, but I believe that the spec doesn't require disabled inputs to have the appropriate contrast?

The color contrast of this doesn't pass, but I believe that the spec doesn't require disabled inputs to have the appropriate contrast?

Correct. No contrast requirement for disabled items.


Enable fp8e5m2fnuz type

Enables the E5M2 FNUZ datatype so that we have full support for all the current FP8 types
E5M2 FNUZ will not be used directly in model but might be useful when converting from OCP -> FNUZ
Lots of updated files, but mostly expanding test cases

Should get this in sooner than later @causten . Onnxrt has support for this as well form the looks of it so it would be nice to get his all in for fp8 support at once


[ts-registry] Add JPEG-LS pixel data encoder

With decoding provided in #534, this PR now adds encoding, also through CharLS.
Summary

rename JpegLSAdapter to JpegLsAdapter
impl PixelDataWriter for JpegLsAdapter

uses charls-rs all the same, uses a transformation function to turn quality and sample bit depth into the NEAR parameter.

add JpegLsLosslessEncoder, which uses the same encoder implementation but overrides quality to 100 (lossless)
update entries module and crate root documentation accordingly
add tests for JPEG-LS encoding and decoding
[toimage] infer JPEG-LS image unwrapping to extension .jls

Just made these changes:

if samples per pixel is 1, photometric interpretation is set to MONOCHROME2 only if it is not one of MONOCHROME1, MONOCHROME2, or PALETTE COLOR
force lossless encoding if the source pixel data photometric interpretation is PALETTE COLOR

I like this approach, and it will keep things from breaking.

Just made these changes:
* if samples per pixel is 1, photometric interpretation is set to `MONOCHROME2` only if it is not one of `MONOCHROME1`, `MONOCHROME2`, or `PALETTE COLOR`

* force lossless encoding if the source pixel data photometric interpretation is `PALETTE COLOR`

* rebase

This should work great

Thanks for the review!


MissingPluginException (MissingPluginException(No implementation found for method read on channel plugins.it_nomads.com/flutter_secure_storage))

MissingPluginException (MissingPluginException(No implementation found for method read on channel plugins.it_nomads.com/flutter_secure_storage))
Not sure what happened, but I've been getting the title error every time I try to run my app. I removed the plugin files from my .pub_cache but the problem persists.  I don't think I'm doing anything out of the ordinary.  I've tried on multiple emulators and a physical device, but I just cannot get this to build.
final storage = new FlutterSecureStorage();
String accessToken = await storage.read(key: 'access_token'); // <-- error

This wasn't a problem until today.  I think the only thing that might've borked my app would be doing a git checkout but I'm not sure.

Hi @Kyle-Mendes
is it iOS or Android?
Flutter has such issue from time to time. You need to force dependency update, e.g. add new plugin , get packages and remove the plugin.

That doesn't seem to have worked, unfortunately
    • Flutter version 1.3.8 at /Users/user/Projects/flutter
    • Framework revision e5b1ed7a7f (5 weeks ago), 2019-03-06 14:23:37 -0800
    • Engine revision f4951df193
    • Dart version 2.2.1 (build 2.2.1-dev.0.0 571ea80e11)

[✓] Android toolchain - develop for Android devices (Android SDK version 28.0.3)
    • Android SDK at /Users/user/Library/Android/sdk
    • Android NDK location not configured (optional; useful for native profiling support)
    • Platform android-28, build-tools 28.0.3
    • Java binary at: /Applications/Android Studio.app/Contents/jre/jdk/Contents/Home/bin/java
    • Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)
    • All Android licenses accepted.

[!] iOS toolchain - develop for iOS devices (Xcode 9.2)
    • Xcode at /Applications/Xcode.app/Contents/Developer
    • Xcode 9.2, Build version 9C40b
    ✗ libimobiledevice and ideviceinstaller are not installed. To install with Brew, run:
        brew update
        brew install --HEAD usbmuxd
        brew link usbmuxd
        brew install --HEAD libimobiledevice
        brew install ideviceinstaller
    ✗ ios-deploy not installed. To install:
        brew install ios-deploy
    ! CocoaPods out of date (1.5.0 is recommended).
        CocoaPods is used to retrieve the iOS platform side's plugin code that responds to your plugin usage on the Dart side.
        Without resolving iOS dependencies with CocoaPods, plugins will not work on iOS.
        For more info, see https://flutter.io/platform-plugins
      To upgrade:
        brew upgrade cocoapods
        pod setup

[✓] Android Studio (version 3.0)
    • Android Studio at /Applications/Android Studio.app/Contents
    • Flutter plugin version 22.2.1
    • Dart plugin version 171.4424
    • Java version OpenJDK Runtime Environment (build 1.8.0_152-release-915-b08)

[✓] VS Code (version 1.33.0)
    • VS Code at /Applications/Visual Studio Code.app/Contents
    • Flutter extension version 2.25.0

[✓] Connected device (2 available)
    • Android SDK built for x86 • emulator-5554                        • android-x86 • Android 8.0.0 (API 26) (emulator)
    • iPhone X                  • AFE355F9-BD65-4E01-AD21-956C7163274B • ios         • iOS 11.2 (simulator)

! Doctor found issues in 1 category.

I found this comment. Can you check
https://github.com/flutter/flutter/issues/14137#issuecomment-447336721 ?

Just tried removing all of ios and android.  Ran flutter create . and then updated the gradle file to have the minSdk for this package.  I'm still encountering the title error however :(

Did you experience the same issue with another package with native plugins? Can you try any new package , eg Firebase or image pickers ?

I just tested a very simple app using the image_picker that you shared before, and was able to get it to run.
import 'package:flutter/material.dart';
import 'package:image_picker/image_picker.dart';

void main() => runApp(MyHomePage());

class MyHomePage extends StatefulWidget {
  @override
  _MyHomePageState createState() => _MyHomePageState();
}

class _MyHomePageState extends State<MyHomePage> {
  var _image;

  Future getImage() async {
    var image = await ImagePicker.pickImage(source: ImageSource.camera);

    setState(() {
      _image = image;
    });
  }

  @override
  Widget build(BuildContext context) {
    return MaterialApp(
        home: Scaffold(
      appBar: AppBar(
        title: Text('Image Picker Example'),
      ),
      body: Center(
        child: _image == null ? Text('No image selected.') : Image.file(_image),
      ),
      floatingActionButton: FloatingActionButton(
        onPressed: getImage,
        tooltip: 'Pick Image',
        child: Icon(Icons.add_a_photo),
      ),
    ));
  }
}

I actually think I might have fixed it!
I manually removed the app from my emulator (went to the app drawer, long pressed, app info, uninstall) and it seems to be building again.
Thanks for the help in debugging this!

that’s great,
you are welcome.

@Kyle-Mendes That also worked for me when nothing else was

Please also check your .kt file in android src which look likes:
`import android.os.Bundle
import io.flutter.app.FlutterActivity
import io.flutter.plugins.GeneratedPluginRegistrant
class MainActivity: FlutterActivity() {
override fun onCreate(savedInstanceState: Bundle?) {
super.onCreate(savedInstanceState)
GeneratedPluginRegistrant.registerWith(this)
}
}`

After few hours of surfing. Finally SOLVED for me. Here is what I found out.
If you are calling flutter_secure_storage (or any packages) method in background service (as example, when you are using notification onBackgroundMessage). This exception occurred because usually our plugin registered at main.dart in foreground, but if we are calling our plugin's method in background we need to manually registered our plugin in our app/src/main/[kotlin/java]/.../Application.[java or kt].
Inside the Application.java or Application.kt

After done that, do flutter run again. Hope it helps!


Is there a way to update Chrome and Firefox version in testcafe docker?

Are you requesting a feature or reporting a bug?
What is the current behavior?
Running tests on testcafe docker works fine, but the browser versions are not latest.
What is the expected behavior?
Run on latest chrome and firefox version.
How would you reproduce the current behavior (if this is a bug)?
pull the docker image and run tests
Provide the test code and the tested page URL (if applicable)
$ docker run -v /Desktop/ci-integration-demo/tests:/tests -it testcafe/testcafe 'chromium --no-sandbox,firefox' /tests/test.js
Running tests in:

Chrome 64.0.3282 / Linux 0.0.0
Firefox 58.0.0 / Linux 0.0.0

A set of examples that illustrate how to use TestCafe API
✓ Text typing basics
✓ Click an array of labels and then check their states
✓ Dealing with text using keyboard
✓ Moving the slider
✓ Dealing with text using selection
✓ Handle native confirmation dialog
✓ Pick option from select
✓ Filling a form
8 passed (25s)
Tested page URL: https://github.com/VasilyStrelyaev/ci-integration-demo/tree/master/tests
Test code

Specify your

operating system: docker container
testcafe version:
node.js version:

Hi @sachs7, currently only Chrome 64 & Firefox 58 are available in Alpine repositories: chromium, firefox. Unfortunately, you have to build your own Ubuntu/Debian/Arch based image, if you want to use Firefox 59 & Chrome 65.

I will update the official image as soon as updated browser versions will appear in the repository

@sachs7 - if you want something to tide you over, here is our homegrown dockerfile that is focused on Local Headless Chrome + Remote Browsers [browserstack / saucelabs].
We add our code during build, you can change that by simply commenting out the COPY . /
FROM node:9-slim

# See https://crbug.com/795759
RUN apt-get update && apt-get install -yq libgconf-2-4

# Install latest chrome dev package and fonts to support major charsets (Chinese, Japanese, Arabic, Hebrew, Thai and a few others)
# Note: this installs the necessary libs to make the bundled version of Chromium that Puppeteer
# installs, work.
RUN apt-get update && apt-get install -y wget --no-install-recommends \
    && wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - \
    && sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google.list' \
    && apt-get update \
    && apt-get install -y google-chrome-unstable fonts-ipafont-gothic fonts-wqy-zenhei fonts-thai-tlwg fonts-kacst ttf-freefont \
      --no-install-recommends \
    && rm -rf /var/lib/apt/lists/* \
    && apt-get purge --auto-remove -y curl \
    && rm -rf /src/*.deb

RUN npm i -g testcafe

COPY package.json package.json
COPY package-lock.json package-lock.json

RUN npm install \
    && rm -rf /tmp/*

COPY . /

RUN chmod +x /entrypoint.sh

# Add user so we don't need --no-sandbox.
RUN groupadd -r testcafe && useradd -r -g testcafe -G audio,video testcafe \
    && mkdir -p /home/testcafe/Downloads \
    && chown -R testcafe:testcafe /home/testcafe \
    && chown -R testcafe:testcafe /node_modules

# Run everything after as non-privileged user.
USER testcafe

ENTRYPOINT ["testcafe"]
CMD ["-h"]

@AndreyBelym - we have some learning from trying to work with the official image if you are willing to discuss. We think we can contribute some more robust docker interfaces for TestCafe.

Awesome @tk8817 I will try it out! Also, is there a way wherein you can point the Git Repo to fetch the tests. Something like:
docker run -v <https://github.com/some/repo>:/tests -it testcafe/testcafe -c 6 'chromium --no-sandbox' /tests/test.js -S -s /tests/screenshot

Hi @tk8817, of course I'll be happy to get your feedback and learn something from it 👍

The question was answered - https://github.com/DevExpress/testcafe/issues/2278#issuecomment-379763423

@tk8817 thanks for the script. i am struggling to run my test in the docker and i'm using this command
docker run -v ${PWD}:/tests node:9-slim chrome '/tests/tests/**/*'
could please tell me what i'm doing wrong?

@augustineuzokwe, try this
docker run --rm -it --shm-size=1gb testcafe:custom  puppeteer:no_sandbox tests/**/*
In my prior comment I accidentally used your testcafe arguments not realizing that my image uses puppeteer rather than chrome in headless mode. Puppeteer is the official Google repo for working with Chrome programatically.
A couple notes:

you don't need to mount in your tests because they are brought in during the Docker build step.
I have addd the --rm flag which removes the container when its done executing
I have added the -it tflag which gives you an interactive tty shell
I have added the --shm-size=1gb flag which is a trick to keep Chrome happy in Docker

Thanks @tk8817, I feel I should add --shm-size=1gb to the documentation.

Hi @tk8817 first of all, thanks for sharing this. I am running your Dockerfile image but I have the same issue mentioned before by @augustineuzokwe.
While executing ..
docker run --rm -it --shm-size=1gb testcafe:custom puppeteer:no_sandbox tests/**/*
I'm getting ..
ERROR Unable to find the browser. "puppeteer:no_sandbox" is not a browser alias or path to an executable file.
But also, trying with chrome, the process got hung and after I stop the process, the error thrown is the following:
ERROR Unable to establish one or more of the specified browser connections. This can be caused by network issues or remote device failure.
Any idea what is happening?

@alxtgda, when you use chrome in a Docker container, you should specify the ---no-sandbox flag for Chrome (starting it as docker run ... testcafe/testcafe 'chrome --no-sandbox') or starting the Docker container in the privileged mode using the --privileged flag (docker run --privileged ...).

The only way I managed to get it running was to use chrome:headless . My guess is that I'm missing some xvfb configuration to have a graphical term.
docker run --rm -it --privileged --shm-size=1gb testcafe:custom_v1 'chrome:headless' tests/**/*
However I'm still experimenting a lot of flakyness running it on the container in comparison with running it locally.

@tk8817 Hey, I am also experiencing flakyness with testcafe's docker image.
It's mostly solved when using --shm-size=4gb but I'm interested in understanding why it helps?
@AndreyBelym  ?

Hi @amits1995, this switch controls size of the /dev/shm pseudo-file inside a Docker container. /dev/shm represents shared memory, that can be used for inter-process communications (IPC) and for high-speed temporary data storage, e,g. for storing browser's cache. Google Chrome actively uses shared memory, so increasing /dev/shm size helps in avoiding shared memory overflow.
I've found that since Chrome 65, you can tell the browser to not use shared memory by specifying the --disable-dev-shm-usage switch: Google Chrome in Docker tips.  It will be nice if you check if this switch works for you and report the result here. It's a browser switch, so it must be specified to the TestCafe image like:
docker run -it testcafe/testcafe 'chromium -- no-sandbox --disable-dev-shm-usage' tests

Yep, tests are way more stable now with --disable-dev-shm-usage
Though I still have random issues with screenshots not being taken sometimes (usually because of a page redirect) but that's a different issue probably.
For the protocol, the error we used to see before using --disable-dev-shm-usage is:
ERROR The HeadlessChrome 68.0.3440 / Linux 0.0.0 browser disconnected. This problem may appear when a browser hangs or is closed, or due to network issues

Maybe it's worth updating this documentation


Add hints (#[diagnostic::on_unimplemented]) to required interface required by tracing feature

To use tracing is required to implement a trait to log register access.
It would be easier to use if there is a informative message to explain what to implement in case of of missing implementation
Describe the solution you'd like
Use  diagnostic attribute

The attribute doesn't really apply to our use case: we don't have a trait that we could mark since we add read/write/read-modify-write callback separately.


V1.1 login/signup with orders

Merged and resolve conflicts

Changes look good to merge in! Really good job :)
Carried over from #18 but fixing conflicts


CLI does not run anymore - xdg 'require_relative': cannot load such file error

Error when gem is installed:
Traceback (most recent call last):
        10: from /usr/local/bundle/bin/conjur:23:in `<main>'
         9: from /usr/local/bundle/bin/conjur:23:in `load'
         8: from /usr/local/bundle/gems/conjur-cli-6.0.0/bin/conjur:24:in `<top (required)>'
         7: from /usr/local/lib/ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'
         6: from /usr/local/lib/ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'
         5: from /usr/local/bundle/gems/conjur-cli-6.0.0/lib/conjur/cli.rb:25:in `<top (required)>'
         4: from /usr/local/lib/ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'
         3: from /usr/local/lib/ruby/2.6.0/rubygems/core_ext/kernel_require.rb:54:in `require'
         2: from /usr/local/bundle/gems/xdg-2.2.4/lib/xdg.rb:26:in `<top (required)>'
         1: from /usr/local/bundle/gems/xdg-2.2.4/lib/xdg.rb:28:in `<module:XDG>'
/usr/local/bundle/gems/xdg-2.2.4/lib/xdg.rb:28:in `require_relative': cannot load such file -- /usr/local/bundle/gems/xdg-2.2.4/lib/xdg/index (LoadError)

Looks to be caused by xdg 2.2.4 gem. Pin to 2.2.3 makes the CLI work again.

Fix released with v6.2.1


ODS: Employee record not passed with form submission to ODS/BI

When the Telework form data is sent back to us, the EMPL_RCD is lost. This makes calculating/assigning the EMPL_RCD tricky especially in the cases where employees have multiple records.

@T854236 Hi Patrick - can we connect about this ticket so I can understand timelines and if this can be pulled into the backlog. Thanks. Do we need Steven Jones for this if this involves the dashboard?

@MeghanStothers
Hi, I was away on vacation but will book a meeting with Aki.

@T854236, can you provide an estimate for this ticket?  There are no Devs assigned...

@Abuchana we would need input from a forms developer for the effort.  The job record already exists in the API endpoint being consumed.

@T854236, are you thinking PSA Dev or EY Dev?

@Abuchana I suppose that depends on who can add a new field on the form from the API endpoint.  I'm not sure if a PSA dev does that now?

@HasanSifat, who would be the dev on this ticket? TES Dev or PSA Dev? we need to assign it accordingly...

For now, this would be Dev-PSA and that is because we still are looking into solutions to this particular issue. But not a priority for the next sprint or at least till SL review launch.

@HasanSifat thank you. So pull it into the product backlog and assign it to...?

yes product backlog and assigned to Me/Stella. I see Patrick is already tagged.

PDP project team is also facing this same issue.

@T854236 any news or solutions to this?

@HasanSifat the employee record is available in the existing endpoint for employee demographic to be consumed by the application.  The application will need to have logic to determine what is passed back down to ODS and BI.

Setup meeting with Patrick to discuss implication of having an employee with 2 diff positions (i.e. 2 different records in the database).

Does this mean they have 2 different supervisors, and should be allowed to have 2 different agreements?
How do we want to handle this situation for these employees?

Closed because it affects only reporting and there are a very small fraction of people with this issue.


Save summary on the last message

This is an attempt to fix this issue.
I couldn't quite replicate this locally, but the test should put it in the state that I noticed.
Description

What happened here is that the history and pruned_memory arrays were being cleared because of the while loops running too long. This happens because the summary + history + promtp are all very large (token wise). Previously we didn't save the summaries that were being generated on any message, but now we just save it on the latest message.
User Impact

My guess is better suited responses? It's unclear.

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:
Additional details and impacted files

:loudspeaker: Thoughts on this report? Let us know!


Set up dev environment (Nick)

I view this issue as getting my local dev environment functionally connected to both our data bases and our github. The github connection will be straight forward, and I don't anticipate too much difficulty using the log in that Noah provided me to get onto their server (the name escapes me as I am writing this description).

I completed the connection to the github. But I now need to locally "clone" ARC databases.

Done!


Bot can't perform sleep action because id is not readable

I wanted to create bot that would perform sleep action, to do it I need id of that bot. Even when I give the right id I still get an error
My code:
const bedrock = require('bedrock-protocol')
const client = bedrock.createClient({
 realms: {
   pickRealm: (realms) => realms[0]
   }
})

client.on('join', () => { // The client has joined the server.
   // client.on('start_game', console.log)
   client.queue('player_action', { action: 5, runtime_entity_id:<PHONE_NUMBER>, position: 0, face: 0 })
})

Error:
https://pastebin.com/BEpFfvf0

You are serializing the packet wrong. position: 0 is not valid ; it must contain proper coordinates.
See the protocol documentation https://minecraft-data.prismarine.js.org/?v=bedrock_1.19.21&d=protocol#packet_player_action

Well, now I have correct cordinates but I still get an error : /
const bedrock = require('bedrock-protocol')
const client = bedrock.createClient({
  realms: {
    pickRealm: (realms) => realms[0]
    }
})

const position = {
      x: 181,
      y: 58,
      z: 2926
}

client.on('join', () => {
    // client.on('start_game', console.log)
  client.queue('player_action', {
    action: 5,
    runtime_entity_id:<PHONE_NUMBER>,
    position: position,
    face: 0
  })
})

maybe I'm doing something wrong again but according to the docs I don't think so


Dotnet seems not trigger

Hello,
i create a plugin for gradle gradle-license_finder-plugin whe i use that on java project (gradle) work fine, but with dotnet project i see that
Task :reportLicensesToJson
LicenseFinder::Dotnet: is active
LicenseFinder::Dotnet: is not installed

when i run directly on my machine  i see
LicenseFinder::Dotnet: is active
LicenseFinder::Dotnet: is installed

so i decide to check command generate by gradle plugin  and i have that license_finder --project-path=./src so when i run this command into my gradle plugin i can't see licenses of my dependencies but when i run directly on my machine same command i see all licenses of dependencies.
Any idea ?

@josselinchevalay I think there are two things going on here. For the gradle part, make sure you are following the Gradle Projects part of the README.md.
For the dotnet thing, we will need to look into why the dotnet library is not installed in the LicenseFinder docker image. Do you have a sample dotnet project that you were working on that you could give us to try out? Thanks!

@josselinchevalay Could you please tell us if the system you ran license_finder had dotnet installed?
For license finder, a project is active if it contains relevant package manager files(*.csproj in this case). So even though dotnet command is not present, a project will be reported as active but license finder will also print the status for package management command not installed.
The license finder docker image has these installed, is that where you are running license_finder?

good morning,
I'll give you a little context. In my company we're based on javaists. But we've had to do DotNet projects for clients. Since we are very java oriented we build all our projects with gradle even DotNet projects we have created a gradle plugin for msbuild. On my machine for example if I run license_finder directly on a java project + gradle it works fine, if I always run a live gralde project + DotNet it works too. but we need in our build process to integrate your license report in our package and for that we have open sourcer a gradle plugin to run the command license_finder in a gradle process the code is here. with this plugin the java + gradle project works well but in this case the DotNet + gradle project doesn't work. so I summarize:

live (I open a command line and launch license_finder) both cases works.
In gradle (the process gradle [process java]) launches the command which it enriches with parameters: works only in the case java + gradle.

let me know if you need more details
Regards

It sounds difficult to reproduce your unique use case.
Would you be able to provide a sample project? A minimal public repo for a dotnet project with a gradle file that uses your plugin, plus the command you would run to reproduce the issue.

I created a sample project with gradle and dotnet you can see the sources here. But it works well in my sample project with gradle and direct command line. I'm a bit confused. I need to discuss with my team about this problem and I'll let you know if I find out why or if I need help. On the other hand now you with a gradle plugin for your project :tada:

intresting thing we use windows as a os and with have on all machine git bash installed and when we run with git bash seems we have the issue. with windows cmd both case seems works


[improve] Upgrade lombok to 1.18.36

Motivation
Keep up-to-date.
Change log: https://projectlombok.org/changelog
Using the 1.18.36 can avoid the following error when using the idea runs the tests directly:
java: Lombok annotation handler class lombok.javac.handlers.HandleToString failed on repo/pulsar/pulsar-broker-common/src/main/java/org/apache/pulsar/broker/ServiceConfiguration.java: java.lang.StackOverflowError

Modifications

Upgrade lombok from 1.18.32 to 1.18.36.

Documentation

[ ] doc
[ ] doc-required
[x] doc-not-needed
[ ] doc-complete

btw. regarding the StackOverflowError, the config in .mvn/jvm.config with -Xss1500k has been a workaround for this problem. We can keep that setting even if Lombok has improved since it's not causing any issues to increase the default stack size from 1MB to 1500kB.
I have forgotten to document this workaround in IntelliJ compiler:

/pulsarbot rerun-failure-checks

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 74.29%. Comparing base (bbc6224) to head (a2400cd).
Report is 799 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master   #23752      +/-   ##
============================================
+ Coverage     73.57%   74.29%   +0.72%
+ Complexity    32624    32115     -509
============================================
  Files          1877     1838      -39
  Lines        139502   143048    +3546
  Branches      15299    16232     +933
============================================
+ Hits         102638   106281    +3643
+ Misses        28908    28406     -502
- Partials       7956     8361     +405

Flag
Coverage Δ

inttests
26.86% <ø> (+2.27%)
:arrow_up:

systests
23.68% <ø> (-0.65%)
:arrow_down:

unittests
73.66% <ø> (+0.81%)
:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.
see 1002 files with indirect coverage changes


Kye

Test.

Here are the Directories, I also added a file for us to work in, and put information as to what content would go in each folder.


Lines and Triangles modules fail timing on iCE40

The Lines and Triangles designs top_cube.sv and top_triangles.sv doesn't meet timing on iCE40.
If the timing constraint is removed from the PCF, the design does build and appears to run successfully on iCEBreaker. However, improving performance is still desirable and we're close to meeting timing:

Cube: ERROR: Max frequency for clock 'clk_pix': 24.76 MHz (FAIL at 25.14 MHz)
Triangles: ERROR: Max frequency for clock 'clk_pix': 22.70 MHz (FAIL at 25.14 MHz)

With the latest display timings and nextpnr, both designs just meet timing:

Cube: Info: Max frequency for clock 'clk_pix': 26.77 MHz (PASS at 25.14 MHz)
Triangles: Info: Max frequency for clock 'clk_pix': 25.17 MHz (PASS at 25.14 MHz)

Leaving this issue open for now as we could still do with a bit more slack on triangles.

With the latest version of draw_line.sv, both top_cube and top_triangles exceed 27.5 MHz on iCEBreaker.


Support gzip Content-Encoding

Nest.JS supports compression, but they suggest not enabling it in the app, but in the application server. Not sure if this is something that can be enabled easily in the Azure portal, but it is worth looking into

For larger reports there are even bigger benefits

By the way @hugo-vrijswijk, would you mind using milestones for future issues/releases?
I like organizing issues this way, curious to know what you think about this 😃.

Yes, of course! I've never used milestones before, but I suppose it makes it easy to plan when to release. It might be useful to add something about it in the contributing.md?


Vaccine zip code endpoint may change weekly

We probably need to use beautifulsoup to find the url on that "Download All" button on this page

These pages have API endpoints we can use, probably no need scrape them.
https://data.chhs.ca.gov/api/3/action/package_show?id=covid-19-vaccine-progress-dashboard-data-by-zip-code

Now using the API to access the metadata about each of the weekly data urls and grab the latest one.

Tested in the scraper and the processor. Looks OK.


Granular HTTP permisisons

It would be nice if we had more control over how and which plugins use HTTP. Currently, we have to compile extism with a feature flag  that enables it for all plugins.
Here are some ideas:

Individual HTTP permissions per plugin
List of permitted domains per plugin (similar to the new filesystem path permissions)

It's easy to miss - we are still working on improving documentation around how to use the manifest fields but the manifest already supports an allowed_hosts field (similar to allowed_paths.)
When this is an empty array then HTTP requests to any host will fail, which could be used to disable HTTP requests.
Would that work for your use case?


Memory issue found in csg_stat when using valgrind

details?

Here the error was found to come from tools:
https://github.com/votca/tools/pull/73

Issues are also being addressed here: https://github.com/votca/csg/pull/283
and here: https://github.com/votca/tools/pull/80

See #294


README_ID.md

Indonesian version

Hey @CaptRoy100
Thanks again for the correction and the new PR!
Unfortunately, here you are still modifying the original Readme.md file. Please create a new file called: README.md.
You can find more instructions below:
https://docs.github.com/en/repositories/working-with-files/managing-files/creating-new-files
Thank you!


Direct DB connection - No data in Grafana 8.0

Describe the bug
No data returned for queries when Direct DB connection enabled. This bug appears in Grafana 8.0.
Probably, something was changed in the SQL data sources response format, because SQL query copied from panel inspector returns data as expected.
Not sure does it make sense to fix it since queries are moving to the backend and there's no ability to use SQL data sources for querying data anymore. Maybe it will be possible in future, but backend queries solve most of problems that Direct DB connection is trying to address.
Software versions

Grafana
Zabbix
Grafana-Zabbix Plugin

8.0.x
x.x.x
4.1.5

So should we simply disable "Direct DB connection" ?

So should we simply disable "Direct DB connection" ?

If it's work for you, you can do it. But understand that without Direct DB you can have some problem with Zabbix API query limits that just throws you a 500 error if you request too much from it.

Well I have some bigger instance where this could be a problem (and I can not test it at the moment).
Thing is I do not understand what this means (do you have any pointer to grafana 8.0 documentation/changes?):

Not sure does it make sense to fix it since queries are moving to the backend and there's no ability to use SQL data sources for querying data anymore. Maybe it will be possible in future, but backend queries solve most of problems that Direct DB connection is trying to address.

So I don't see what alternative to not load the Zabbix API from grafana do we have.

@fauust I mean with the backend load for the backend will be reduced (but not so much as with direct db connection). Also, implementing direct db connection on the backend is tricky since I cannot use existing data source (maybe, I can, but I have to investigate). So my tip:

Disable direct db connection if it's not critical for you (your Zabbix server can handle amount of queries you usually invoke).
Downgrade to Grafana 7.5 and wait for the fix (will be in 4.2 release).

Great, don't hesitate to ping me if you need help in testing.

Same problem here. :/

Same problem here
I disable direct db connection and wait 4.2 release

I have the same problem "no data"

@jcoliveira-dotcom do not use for now the DB connection.

+1

Closed by #1256


Will the project support U200？

Hope to use it on U200 board.

Currently, OpenNIC supports the U250 and U280 as targets, with a university group currently adding U50 support.  We believe that it should be fairly easy to port the U250 version to U200, and so we encourage any interested person in the community to do this.

also interested by u50 support. is it possible to reach the university group ?

In terms of the port for the U50 board, there is some brief info within this post:
https://github.com/Xilinx/open-nic-driver/issues/4


Confusion about the SB-CFM

Thank you for your contribution, I have some confusion about SB-CFM, I find when I remove OT, the results are better than with OT in my task.  As discussed in the issue, I am also a condition-generating task, if the method in the original article still right after removing OT. I can't understand the derivation in your paper, especially Equation 19. It still seems to be correct even if the OT is removed, but not sure, so I'm asking for your advice, looking forward to your reply!

thanks very much!


Slot for the content

Problem
The content of the VTag should be in a slot.
Description
Use a slot for the content instead of a prop. This can unlock future UI additions/improvements such as icons to indicate ML-generated tags etc.

Closed with a4d5f8b


Make test suite work with local git configs

On my work laptop, I was seeing failures in spec/commands/newgem_spec.rb due to the presence of  local .git/config files.
On my work computer, my global config is my work (private gitlab) credentials. Each github repo has a local config with my “cdwort” credentials. For example, I have one placed in /Path/To/Bundler/.git/config.
Unfortunately, when a new gem is created within the test file noted above, it is created within the /Path/To/Bundler/ directory. This means it picks up my local config. All the tests for when there is no git config information fail because instead of getting nothing (which those tests expect because the test overrides my global<EMAIL_ADDRESS>setting), it gets my GitHub email.
I am using the --remove-section flag because if you only --unset user.email and --unset user.name, you get the following junk in your .git/config file. Yes, at the very bottom is the appropriate config.

This has one drawback - it rearranges your file.  This places it at the bottom of the file, because the section is removed and then recreated each time for each test.
I'll take that trade-off for running my tests on my work laptop, but I can see that this is unexpected behavior and might prohibit this PR from going forward. Thoughts?

Oooooh actually, maybe we could use the GIT_CONFIG environment variable to force it to use a scratch file?

Yes, if that's a thing! Not sure from looking at this: https://git-scm.com/book/en/v2/Git-Internals-Environment-Variables

from man git-config
ENVIRONMENT
       GIT_CONFIG
           Take the configuration from the given file instead of .git/config. Using the "--global" option forces this to ~/.gitconfig. Using the "--system"
           option forces this to $(prefix)/etc/gitconfig.

       GIT_CONFIG_NOSYSTEM
           Whether to skip reading settings from the system-wide $(prefix)/etc/gitconfig file. See git(1) for details.

Oh, danke. I'll look into that tomorrow. That sounds like a far better option.

Alright, so this is now working without altering either the global or the local config.
It does not:

Alter the user's global git config
Alter the user's local git config
Alter the "GIT_CONFIG" env variable

It does, however, cause the test suite to be littered with:
fatal: BUG: lockfile filename corrupt
fatal: BUG: lockfile filename corrupt
fatal: BUG: lockfile filename corrupt

I'll work on that if this looks like a strategy we want to pursue. Personally, I think this is cleaner than mucking about in the user's config files.

If we can do this without messing with user files, that would be great. 👍 from me

Yeah, it's a tradeoff, but I'm happier messing with environment variables than I am with messing with files.

Err, I suppose my comment above needs clarification:
With this PR, this file now does not:

Alter the user's global git config
Alter the user's local git config
Result in a change of the "GIT_CONFIG" env variable once the after block is run.

Test suite is happy now locally, without code alteration.
I was altering ENV variables on the command-line and had a beautiful moment where I forgot that setting a variable to empty string is not the same as unseting it.
@segiddins @indirect If the above looks :+1: then can we get a CI build? Also, would you like the two commits on this PR squashed?

Normally, I'm pretty indifferent to squashing, but in this case the second commit is by "Foo Bar", so a squash would be good. :)

Yay, looks great @cdwort ! Will :+1: when squashed.

Hm, seems like Rubocop is unhappy about single quotes even though by the message, I don't think it should be:
spec/commands/newgem_spec.rb:31:16: C: Style/StringLiterals: Prefer double-quoted strings unless you need single quotes to avoid extra backslashes for escaping.
    `rm "#{ENV['GIT_CONFIG']}"` if File.exist?(ENV["GIT_CONFIG"])
               ^^^^^^^^^^^^

I'll fix, but I wonder if Rubocop is confused by the backtic?

Oh. It's not confused by the backtick—we have rubocop set to enforce double-quotes everywhere (and double quotes inside interpolation inside double quotes don't need to be escaped).

Heh, yup, just realized the latter point.

All traces of Foo Bar gone! Should be ready for CI.

@homu r+

:pushpin: Commit 1c32a71 has been approved by indirect

:hourglass: Testing commit 1c32a71 with merge 279c2f7...

:broken_heart: Test failed - status

@homu retry

:hourglass: Testing commit 1c32a71 with merge 854fd9b...

:sunny: Test successful - status


Paper revision

@mikelove we could meet briefly today to discuss the messages that emerged from the paper, which should definitely be very clear and strong in the paper.
I listed some I noticed

[x] tidyomics, while offering a bridge to the rich tidyverse ecosystem, do so, leaving Bioconductor infrastructure untouched, so users can choose when switching between tidy or standard paradigms interchangeably.
[x] tidyomics does not create or alter any of the data containers that are pillars of the Biocnoducotor platform. Therefore, developers can still rely on the maintainability and support that the Bioconductor infrastructure offers.
[x] tidy (and tidyomics) code is more readable
[x] The use of a small number of verbs simplifies learning. The data representation and consistent/shared grammar encourage the use of 'pipes' to assemble a short series of operations into a compact, legible transformation.
[x] The tidy grammar and syntax are de-facto common knowledge in data science. A common tidy API practically lower the barrier-to-entry for the diverse landscape of comic frameworks
[x] make  tidy feature very explicit: (1) Data is always presented as a 'tibble' (data.frame) organizing variables as columns and observations as rows. (2) Data transformation emphasizes a small number of operations ('verbs') that are isomorphic in their first argument -- input and output same consistent properties/structure, increasing modularity and reuse.
[ ] Trasparency statement

Hello @mikelove and @william-hutchison, I have reduced the article to 1300 words, which I think is enough for submission.
The cover letter is ready.
@william-hutchison could you please collect all contacts (affiliation, email and ORCID) of the researchers that contributed to the challenges?
After this, we might submit?
Let me know your thoughs.

Great. I’ll proof tomorrow morning. I reached out to Stuart to ask if he wants to be involved.

I started this list here btw
https://docs.google.com/spreadsheets/d/19XqhN3xAMekCJ-esAolzoWT6fttruSEermjIsrOFcoo/edit#gid=0

The new paper looks great. Do you want me to email the Bioconductor folks again, that we are nearing submission?

Sure!


Proposal: add toLowerCase() and toUpperCase()

String.prototype.toLowerCase() and String.prototype.toUpperCase() are typed as returning string. This doesn't make use of the relatively recently added Uppercase<T> and Lowercase<T> types in TypeScript.
I propose adding two functions to this library:
function toLowerCase<T extends string>(string: T): Lowercase<T>;

function toUpperCase<T extends string>(string: T): Uppercase<T>;

If both methods should be added, I propose adding endsWith, startsWtih, padEnd, padStart, repeat, trimEnd, trimStart, trim and so on. https://github.com/microsoft/TypeScript/blob/main/tests/cases/conformance/types/literal/templateLiteralTypes1.ts

How would using this method over String.prototype.toLowerCase() improve your code? Strict types are great, but they got to have a purpose.

Personally I don't have any use case for either of the proposed case functions. However there are surely developers who could benefit from using one of them instead of just asserting the type after using the built-in method.

Let's keep this open for more feedback. I would like to see more realistic use-cases.


Uncompressed or SASS css dist

Hi there!
Would be possible to public uncompressed css in the dist folder?
During development, usually the uncompressed version is imported.
Also, would be nice a sass version for the css's ;)
Best regards,
Rafael Pacheco.

See gulpfile.js:
gulp.task('less', function () { ...
Just comment out  .pipe(cssmin()).on('error', errorHandler)... and you will get the uncompressed css file.
I'll also switch to SASS eventually because it seems more popular

Thanks!
Indeed SASS seems more popular.
Best regards.

I don't see this(af319b8) commit back in the current version, is SASS removed from the project?

It was changed to http://stylus-lang.com/ :disappointed:

Stylus is also great. I had to convert the styles to .scss for my current project. If you like I could make a pull request with the converted .scss styles.

Love the project + docs, but upvoting to include a /dist folder. This really helps for prototyping. Needing to compile Typescript and Stylus to get working JS and CSS is a hurdle (nay, a dependency).
I would've preferred SCSS over Stylus too. It's just harder to convert to a superset of CSS (SCSS/LESS) for anyone not using Stylus.

Here is a tentative of manual conversion from Stylus to Sass (the CSS produced from the .scss file is 99% the same as the the CSS file found in the distribution).
A converter from Stylus to Sass can be found on npm, but the conversion of the flatpickr.styl document was crashing the converter.
_flatpickr.scss.txt

Thank you!
I think it would be nice if the author include a folder with the scss files, even if they are converted like the latter ones that parisiam gave us. otherwise we must include the library manually outside of npm or similar to make use of the variables.


Statevector.from_instruction with controlled opaque gates breaks

Information

Qiskit Terra version: 0.16.0 (stable)
Python version: 3.7.7 (also on 3.8.3)
Operating system: macOS Catalina

What is the current behavior?
Simulating a circuit containing a controlled circuit with the Statevector class yields all zero amplitudes.
x = QuantumCircuit(1)
x.x(0)
circ = QuantumCircuit(2)
circ.append(x.to_gate().control(), [0, 1])
print(Statevector.from_instruction(circ))  # [0 0 0 0]
print(execute(circ, Aer.get_backend('statevector_simulator')).result().get_statevector())  # [1 0 0 0]

This is the case for different circuits, not just with a single X gate. Not calling control on the gate works correctly.

This gives me the correct result. Using Python 3.8 and qiskit 0.19.6

Hm, maybe this worked earlier, now it doesn't give zero amplitudes but breaks. I think this is a know bug with the quantum info due to nested quantum registers.
>>> from qiskit import QuantumCircuit
>>> from qiskit.quantum_info import Statevector
>>> x = QuantumCircuit(1)
>>> x.x(0)
>>> circ = QuantumCircuit(2)
>>> circ.append(x.to_gate().control(), [0, 1])
>>> print(Statevector.from_instruction(circ))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jul/Work/Qiskit/qiskit-terra/qiskit/quantum_info/states/statevector.py", line 529, in from_instruction
    return Statevector._evolve_instruction(vec, instruction)
  File "/Users/jul/Work/Qiskit/qiskit-terra/qiskit/quantum_info/states/statevector.py", line 690, in _evolve_instruction
    Statevector._evolve_instruction(statevec, instr, qargs=new_qargs)
  File "/Users/jul/Work/Qiskit/qiskit-terra/qiskit/quantum_info/states/statevector.py", line 690, in _evolve_instruction
    Statevector._evolve_instruction(statevec, instr, qargs=new_qargs)
  File "/Users/jul/Work/Qiskit/qiskit-terra/qiskit/quantum_info/states/statevector.py", line 661, in _evolve_instruction
    return Statevector._evolve_operator(statevec, Operator(mat), qargs=qargs)
  File "/Users/jul/Work/Qiskit/qiskit-terra/qiskit/quantum_info/states/statevector.py", line 642, in _evolve_operator
    np.reshape(statevec.data, pre_tensor_shape), axes), contract_shape)
  File "<__array_function__ internals>", line 6, in transpose
  File "/Users/jul/anaconda3/envs/py377/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 651, in transpose
    return _wrapfunc(a, 'transpose', axes)
  File "/Users/jul/anaconda3/envs/py377/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc
    return bound(*args, **kwds)
ValueError: axes don't match array
>>>

Closing as resolved by #5286 .


Mat 4694 create new test case modal

MADiE PR
Jira Ticket: MAT-4694
(Optional) Related Tickets:
Summary
All Submissions

[x] This PR has the JIRA linked.
[x] Required tests are included
[x] No extemporaneous files are included (i.e Complied files or testing results)
[x] This PR is into the correct branch.
[ ] All Documentation as needed for this PR is Complete (or noted in a TODO or other Ticket)
[ ] Any breaking changes or failing automation are noted by placing a comment on this PR.

DevSecOps
If there is a question if this PR has a security or infrastructure impact, please contact the Security or DevOps engineer assigned to this project to discuss it further.

[x] This PR has NO significant security impact (i.e Changing auth methods, Adding a new user type, Adding a required but vulnerable package)
[ ] All CDN/Web dependencies are hosted internally (i.e MADiE-Root Repo)

Reviewers
By Approving this PR you are attesting to the following:

Code is maintainable and reusable, reuses existing code and infrastructure where appropriate, and accomplishes the task’s purpose
The tests appropriately test the new code, including edge cases
If you have any concerns they are brought up either to the developer assigned, security engineer, or leads

CreateTestCase.tsx has been renamed to EditTestCase.tsx so there is no conflict.


Truncated file; non-zero exit status; bwa-mem alignment failure

I've seen similar issues to this, but they're closed.  I did update to current development version just before rerunning this and i get the same error.  I will say upfront that it is "possible" that the file may be truncated somehow, lots of movement before analysis, local server -> S3 -> EBS -> bcbio prep merged.
[2016-11-22T15:00Z] System YAML configuration: /usr/local/share/bcbio/galaxy/bcbio_system.yaml
[2016-11-22T15:00Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16
[2016-11-22T15:00Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job
[2016-11-22T15:00Z] Timing: organize samples
[2016-11-22T15:00Z] multiprocessing: organize_samples
[2016-11-22T15:00Z] Using input YAML configuration: /data/SZ_WGS_Meta-merged/config/SZ_WGS_Meta-merged.yaml
[2016-11-22T15:00Z] Checking sample YAML configuration: /data/SZ_WGS_Meta-merged/config/SZ_WGS_Meta-merged.yaml
[2016-11-22T15:00Z] Testing minimum versions of installed programs
[2016-11-22T15:00Z] Timing: alignment preparation
[2016-11-22T15:00Z] multiprocessing: prep_align_inputs
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] Resource requests: ; memory: 1.00; cores: 1
[2016-11-22T15:00Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-11-22T15:00Z] multiprocessing: disambiguate_split
[2016-11-22T15:00Z] Timing: alignment
[2016-11-22T15:00Z] multiprocessing: process_alignment
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] Aligning lane 1_2016-11-21_SZ_WGS_Meta-merged with bwa aligner
[2016-11-22T15:00Z] bwa mem alignment from fastq: 1_NT_Blood
[2016-11-22T15:00Z] samblaster: Version 0.1.23
[2016-11-22T15:00Z] samblaster: Inputting from stdin
[2016-11-22T15:00Z] samblaster: Outputting to stdout
[2016-11-22T15:00Z] samblaster: Opening /dev/fd/62 for write.
[2016-11-22T15:00Z] samblaster: Opening /dev/fd/63 for write.
[2016-11-22T15:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FF...
[2016-11-22T15:01Z] [M::mem_pestat] (25, 50, 75) percentile: (444, 614, 2476)
[2016-11-22T15:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 6540)
[2016-11-22T15:01Z] [M::mem_pestat] mean and std.dev: (1483.12, 1394.07)
[2016-11-22T15:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 8572)
[2016-11-22T15:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-11-22T15:01Z] [M::mem_pestat] (25, 50, 75) percentile: (510, 594, 690)
[2016-11-22T15:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (150, 1050)
........
[2016-11-22T15:08Z] [M::mem_pestat] mean and std.dev: (2431.38, 1578.82)
[2016-11-22T15:08Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9898)
[2016-11-22T15:08Z] [M::mem_pestat] skip orientation FF
[2016-11-22T15:08Z] [M::mem_pestat] skip orientation RF
[2016-11-22T15:08Z] [M::mem_pestat] skip orientation RR
[2016-11-22T15:08Z] [fputs] Broken pipe
[2016-11-22T15:08Z] [W::sam_read1] parse error at line 97572
[2016-11-22T15:08Z] [bam_sort_core] truncated file. Aborting.
[2016-11-22T15:08Z] [E::sam_parse1] SEQ and QUAL are of different length
[2016-11-22T15:08Z] [W::sam_read1] parse error at line 9942568
[2016-11-22T15:08Z] [main_samview] truncated file.
[2016-11-22T15:09Z] Uncaught exception occurred
Traceback (most recent call last):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /usr/local/share/bcbio/galaxy/../anaconda/bin/bwa mem  -c 250 -M -t 16  -R '@RG\tID:1_NT_Blood\tPL:illumina\tPU:1_2016-11-21_SZ_WGS_Meta-merged\tSM:1_NT_Blood' -v 1 /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /data/SZ_WGS_Meta-merged/work/align_prep/1_NT_Blood_R1.fastq.gz 180000001 200000000) <(grabix grab /data/SZ_WGS_Meta-merged/work/align_prep/1_NT_Blood_R2.fastq.gz 180000001 200000000)  | /usr/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/usr/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 1G -T /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-spl -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpW3_m6g/1_NT_Blood-sort-180000001_200000000-sr.bam /dev/stdin) --discordantFile >(/usr/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 1G -T /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-disc -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmp31ole9/1_NT_Blood-sort-180000001_200000000-disc.bam /dev/stdin) | /usr/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 1G --tmpdir /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-full -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000.bam /dev/stdin
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (411, 586, 1713)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 4317)
[M::mem_pestat] mean and std.dev: (1136.36, 1187.83)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 5888)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (510, 594, 690)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (150, 1050)
[M::mem_pestat] mean and std.dev: (602.11, 140.91)
......
[M::mem_pestat] low and high boundaries for proper pairs: (1, 9898)
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[fputs] Broken pipe
[W::sam_read1] parse error at line 97572
[bam_sort_core] truncated file. Aborting.
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 9942568
[main_samview] truncated file.
' returned non-zero exit status 1
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 230, in
main(**kwargs)
File "/usr/local/bin/bcbio_nextgen.py", line 43, in main
run_main(**kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 127, in variant2pipeline
samples = run_parallel("process_alignment", samples)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, *args, **kwargs)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 80, in process_alignment
return sample.process_alignment(*args)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 113, in process_alignment
data = align_to_sort_bam(fastq1, fastq2, aligner, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 63, in align_to_sort_bam
names, align_dir, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 116, in _align_from_fastq
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.py", line 146, in align_pipe
names, rg_info, data)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bwa.py", line 156, in _align_mem
[do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, fastq_file)])
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /usr/local/share/bcbio/galaxy/../anaconda/bin/bwa mem  -c 250 -M -t 16  -R '@RG\tID:1_NT_Blood\tPL:illumina\tPU:1_2016-11-21_SZ_WGS_Meta-merged\tSM:1_NT_Blood' -v 1 /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa <(grabix grab /data/SZ_WGS_Meta-merged/work/align_prep/1_NT_Blood_R1.fastq.gz 180000001 200000000) <(grabix grab /data/SZ_WGS_Meta-merged/work/align_prep/1_NT_Blood_R2.fastq.gz 180000001 200000000)  | /usr/local/share/bcbio/galaxy/../anaconda/bin/samblaster --addMateTags -M --splitterFile >(/usr/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 1G -T /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-spl -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpW3_m6g/1_NT_Blood-sort-180000001_200000000-sr.bam /dev/stdin) --discordantFile >(/usr/local/share/bcbio/galaxy/../anaconda/bin/samtools sort -@ 16 -m 1G -T /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-disc -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmp31ole9/1_NT_Blood-sort-180000001_200000000-disc.bam /dev/stdin) | /usr/local/share/bcbio/galaxy/../anaconda/bin/samtools view -b -S -u - | /usr/local/share/bcbio/galaxy/../anaconda/bin/sambamba sort -N -t 16 -m 1G --tmpdir /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000-sorttmp-full -o /data/SZ_WGS_Meta-merged/work/align/1_NT_Blood/split/tx/tmpqIJLtg/1_NT_Blood-sort-180000001_200000000.bam /dev/stdin
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (411, 586, 1713)
.....
[M::mem_pestat] skip orientation FF
[M::mem_pestat] skip orientation RF
[M::mem_pestat] skip orientation RR
[fputs] Broken pipe
[W::sam_read1] parse error at line 97572
[bam_sort_core] truncated file. Aborting.
[E::sam_parse1] SEQ and QUAL are of different length
[W::sam_read1] parse error at line 9942568
[main_samview] truncated file.
' returned non-zero exit status 1

Config file:
details:

algorithm:
adapters:

truseq
illumina
align_split_size: 5000000
aligner: bwa
effects: vep
ensemble:
numpass: 3
jointcaller:
gatk-haplotype-joint
platypus-joint
samtools-joint
mark_duplicates: true
mixup_check:
qsignature_full
phasing: gatk
realign: gatk
recalibrate: gatk
remove_lcr: true
save_diskspace: true
svcaller:
lumpy
manta
cnvkit
metasv
svvalidate:
DEL: /home/ubuntu/giab-svclassify-deletions-2015-05-22.bed
INS: /home/ubuntu/giab-svclassify-insertions-2015-05-22.bed
tools_on:
svplots
qualimap_full
bwa-mem
bnd-genotype
gvcf
vqsr
validate: /home/ubuntu/GiaB_v2_19.vcf.gz
validate_regions: /home/ubuntu/GiaB_v2_19_regions.bed
variantcaller:
samtools
platypus
gatk-haplotype
mutect2
varscan
analysis: variant2
description: 1_NT_Blood
files:
/data/merged/1_NT_Blood_R1.fastq.gz
/data/merged/1_NT_Blood_R2.fastq.gz
genome_build: GRCh37
metadata:
batch: T1B
description: null
phenotype: normal

algorithm:
adapters:

truseq
illumina
align_split_size: 5000000
aligner: bwa
effects: vep
ensemble:
numpass: 3
jointcaller:
gatk-haplotype-joint
platypus-joint
samtools-joint
mark_duplicates: true
mixup_check:
qsignature_full
phasing: gatk
realign: gatk
recalibrate: gatk
remove_lcr: true
save_diskspace: true
svcaller:
lumpy
manta
cnvkit
metasv
svvalidate:
DEL: /home/ubuntu/giab-svclassify-deletions-2015-05-22.bed
INS: /home/ubuntu/giab-svclassify-insertions-2015-05-22.bed
tools_on:
svplots
qualimap_full
bwa-mem
bnd-genotype
gvcf
vqsr
validate: /home/ubuntu/GiaB_v2_19.vcf.gz
validate_regions: /home/ubuntu/GiaB_v2_19_regions.bed
variantcaller:
samtools
platypus
gatk-haplotype
mutect2
varscan
analysis: variant2
description: 1_NT_Fibro
files:
/data/merged/1_NT_Fibro_R1.fastq.gz
/data/merged/1_NT_Fibro_R2.fastq.gz
genome_build: GRCh37
metadata:
batch: T1F
description: null
phenotype: normal

Running on amazon m4.4xlarge instance
system config:
cat /usr/local/share/bcbio/galaxy/bcbio_system.yaml
galaxy_config: universe_wsgi.ini
resources:
default:
cores: 16
jvm_opts:
- -Xms750m
- -Xmx3500m
memory: 3G
dexseq:
memory: 10g
express:
memory: 8g
gatk:
dir: /usr/local/share/bcbio/toolplus/gatk/3.6-0-g89b7209
jvm_opts:
- -Xms500m
- -Xmx3500m
macs2:
memory: 8g
qualimap:
memory: 4g
seqcluster:
memory: 8g
snpeff:
jvm_opts:
- -Xms750m
- -Xmx4g

Patrick;
Thanks for the detailed report and apologies about the issues. That's an intense configuration file, I'll try to tackle one thing at a time. Regarding your problem:

The alignment error could be due to a couple of things. Either the input fastqs were corrupt, which you need to manually check (often just by tailing the ends of the files and making sure their are good) or you could be running into problems with samblaster. It appears to have problems on some inputs and we're working on a fix, but the workaround is to avoid using it by removing lumpy from your svcaller list. bcbio will then use a different duplicate marking approach which might work better.

Some other suggestions unrelated to this.

I'm unclear if you're running a tumor/normal somatic analysis or a germline analysis. You have both somatic (mutect2, varscan) and germline (samtools, platypus, gatk-haplotype) in your configuration. You'd want to pick one or the other. I'd also recommend using vardict if somatic calling and freebayes if doing germline calling. If you're doing germline calling you don't need phenotype: normal in your metadata.

Unless you're running a large number of samples (250+) you don't need jointcaller and can remove that from the configuration.

You generally don't need recalibration and realignment and they add a lot of processing overhead. I'd suggest removing these.

If you're not running Genome in a Bottle test data (these look like sample data), the validate targets don't help much since your samples won't be comparable.

Hope this helps with your issue and general configuration.

Thanks for the reply, for context, the analysis is on monozygotic twins that are discordant for a complex disorder using tumor normal phenotype for affected and unaffected twins, so I'm really trying to get super accurate germline and somatic variant calls, there is WGS from blood and from fibroblast for both twins to further tease out germline vs somatic.  I'll drop lumpy to see if samblaster is the culprit.  Thank you for the config suggestions, i'll drop validate and recal/realign.  I'll keep you posted.

removal of lumpy from the config fixed the problem.


Refactor word processors

DON'T MERGE: Should merge after  https://github.com/cofacts/rumors-site/pull/42

Refactors linkify() and nl2br() so that they can be cascaded and allows React element inputs
Adds target="_blank" to out-going links in article & reply pages. Fixes #40
Adds "open new window" icon at the end of target-blank links.

Coverage decreased (-7.3%) to 92.727% when pulling 056bb6812c3913948660729fa9cb89970a973922 on refactor-word-processors into 3243405e1cdf9bf2597f24bf32b7fb55f57a80b4 on add-jest.

Coverage decreased (-7.4%) to 92.593% when pulling 4992f8f896f972651b72f510e7192a56eada493e on refactor-word-processors into 3243405e1cdf9bf2597f24bf32b7fb55f57a80b4 on add-jest.