Could not find package yiisoft/yii2-app with stability dev.

What steps will reproduce the problem?
composer create-project --prefer-dist --stability=dev yiisoft/yii2-app myapp
What's expected?
Create a new project with Yii 2.1
What do you get instead?

[InvalidArgumentException]
Could not find package yiisoft/yii2-app with stability dev.

Additional info

Q
A

Yii version
2.1

PHP version
7.2

Operating system
Ubuntu 16.04

Fixed.


Fix Pac4jOidcClientProperties generic prop type

Fix the generic property type generic. Change from type Pac4jKeyCloakOidcClientProperties to Pac4jGenericOidcClientProperties.

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


Skip generating buf_push rule

Closes #51, before v0.2.0 we choose to not export the buf_push rule but did not skip generating it via gazelle

@srikrsna-buf I just ran into this issue trying to use rules_buf v0.2.0, which is the latest release. Maybe for others it would help to make a point release that includes this fix?


Fixed pin name size on up board

Fixed wrong name size on Up board names
Signed-off-by: Nicola Lunghi<EMAIL_ADDRESS>

Sorry I miss one now should be ok
Thanks
Nicola Lunghi

Merged, thanks!


Feature/consensus/changeable validator set

Change whitelist structure from address => stake to address => true
Revive STAKE env var
Add some safety measures to ensure validator set size >= MIN_NUM_VALIDATORS
Introduce MIN_STAKE_PER_VALIDATOR (its value is subject to change)
Return false if evalRuleString() failed

TODOs

Use a separate json file for genesis params (including genesis whitelist & validators)
Deprecate NUM_VALIDATORS
Remove genesis block & accounts from the source code (once block server is in place?)

Addressed all comments, PTAL @platfowner

Addressed all comments, PTAL @platfowner

Addressed all comments, PTAL @platfowner

Addressed all comments, PTAL @platfowner

Thanks for the review! Now merging..

Thanks for the review! Now merging..


[1.7.10] Observatory not opening up even with station is oriented

LibVulpes-1.7.10-0.2.5-universal
AdvancedRocketry-1.7.10-1.2.2
For awhile, I have been looking around to find how to use the observatory in space. The problem is I cannot get it to open up and program asteroid chips. I oriented the station to where it is the darkest, didn't work.
Thanks

I think it works only on planets, the space stations are not allowed to be used with obs.

Is this still a issue? Please comment if it is and i will reopen if if you are unable? We are closing old issues to see what is still relevant and needs to be fixed.


Display / read .txt files as "Rom notes"

I think it would be great if the browser of cores could display .txt, .jpg (etc.) files.
Why: There are so many great patches around, improving sound, graphics, fixing common bugs, basic quality-of-life, etc. etc. ...when browsing Roms on the APocket it would be great to display / read them as Quick-Info

do you mean on the pocket itself?

do you mean on the pocket itself?

Yes I do...
Scenario:
-- I am browsing through all my roms
-- I want to quickly see what "Rom patch XY" means ...hence I can look at the adjacent .txt file / or screenshot

unfortunately, i have no control over any of that. the analogue firmware is closed source and only maintained by analogue. you'd have to make a feature request with them

Thank you, I appreciate your reply


GMCM Support?

Would it be worthwhile to add in support for GMCM so that the mod can be configured via in game?
https://github.com/spacechase0/StardewValleyMods/tree/develop/GenericModConfigMenu#for-c-mod-authors

Possibly, yea. I don't really use the mod myself so I don't know what users might prefer. Though obviously, at the very least the password should not be editable through the menu ;)

Does it support lists though, such as for the IgnoredAccounts option? I can't really find it.

could add a string field that is manually exploded and repacked that is space separated!

I quickly cooked up this which I'll push in a pull request. You can change the values of the bots that you don't want and it properly restores back into an array. Obviously, if the array is just , then you'll have invalid garbage in the array config, but there's no negative issues there.
I added a password page which is hidden by default and also does not show up in the game (only main menu) where one can put in the OAuth token.
This works, but obviously you would need to restart for any connection changes. However this does make it like a billion times easier for general purpose audiences.
Could also add localization as well.

That looks amazing :) I'll test it myself in a bit and take a look at localization, at least that's something I have done before.
Once more, thank you for your work!

Ah, damn, you're quick. Just noticed you already threw in localization as a bonus. Well, I guess I can handle German localization :')

The main major thing that could be done is to rework the initialization of TwitchBot to execute upon loading a save, rather than on initial entry into the application, allowing for the user to execute their config changes without a restart.
Maybe that's a task for a separate issue.

Sounds reasonable, yea. I'll close this for now.

I'll open a new issue for that.

New issue in #5


Fix error message in VRF P-256 test.

As a follow-up to @Liamsi's comment in https://github.com/google/keytransparency/pull/616, fix the error message in p256_test.go.

Codecov Report

Merging #625 into master will not change coverage.
The diff coverage is n/a.

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##           master     #625   +/-   ##
=======================================
  Coverage   57.21%   57.21%
=======================================
  Files          35       35
  Lines        2489     2489
=======================================
  Hits         1424     1424
  Misses        776      776
  Partials      289      289

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I just noticed that a similar fix is merged in #618. @alsophian can I close this PR unmerged?

Closing this PR is fine with me.


mkdir fix for broken nginx demo app

CLA not necessary for google employee

Hi, can this be merged? The demo app still breaks for this reason and the given fix resolves it.


[usage question] how can I parse a CWL file to the cwlavro model

I would like to parse CWL file into java model classes. I'm using cwl-avro (version: <IP_ADDRESS>) as the model classes. How can I parse the cwl file so that I get back an instance of io.cwl.avro.Workflow.Workflow class
reference

@denis-yuen

@pr80ik
Hi,
There is a test that demonstrates how to parse a file to get back a CommandLineTool https://github.com/common-workflow-language/cwlavro/blob/master/cwlavro-tools/src/test/java/AbstractClientTest.java#L162
Getting back a Workflow is essentially the same, although there isn't a test example of it in this repo.
https://github.com/ga4gh/dockstore/blob/8f4a0cf40214021fbc063e252dde36257b0bcc67/dockstore-webservice/src/main/java/io/dockstore/webservice/languages/CWLHandler.java#L237
Hope that helps!


`umask': no implicit conversion of String into Integer (TypeError)

Description
I have been running this particular cookbook and chef version combination across roughly 50 nodes and it has been working fine until this. It is the only node this happens on. During this process my cookbook updates chef client from 12.x to 14.x
Chef Version
14.2.0
Platform Version
el 6.9
Replication Case
I don't know how to replicate.
Client Output

Stacktrace
A stacktrace is not produced

I checked my config.rb file and had a line defining the umask value. it was 'umask "0022".' I fixed the error by removing the quotes around the number. I guess chef client 12 supported that syntax but 14 does not.


[SPARK-32830][SQL] Optimize Skewed BroadcastNestedLoopJoin with AQE

What changes were proposed in this pull request?
For BroadcastNestedLoopJoin, we will broadcast boradcast-side child to all executor and use stream side partition's data traversal broadcast-side data one-by-one.
We have meet some case that stream side data skew and all success task wait for skewed partition to finish.
We know that the execution time increases exponentially with the amount of partition's data.
If skewd with 100x,  skewed partition's data will execute 100x than non-skewed part.
It is a bottleneck， with AE, we can avoid this by  split skewed part's data  to make it more balanced.
Why are the changes needed?
NO
Does this PR introduce any user-facing change?
NO
How was this patch tested?
Added UT

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ping @cloud-fan @hvanhovell @maryannxue

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retest this please

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Ah, one more comment; could you update the code comment in OptimizeSkewedJoin? It looks most comments assume smj only, e.g.,  https://github.com/apache/spark/pull/29692/files#diff-2d6bea6eed43ca6f37fe3531cb574069R151

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Ah, one more comment; could you update the code comment in OptimizeSkewedJoin? It looks most comments assume smj only, e.g., https://github.com/apache/spark/pull/29692/files#diff-2d6bea6eed43ca6f37fe3531cb574069R151

Updated,  no comment point to SMJ only now.

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What's the high-level idea? We can handle skew SMJ because there is a shuffle and we can split the partition with the granularity of shuffle blocks. Broadcast join doesn't have shuffles.

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What's the high-level idea? We can handle skew SMJ because there is a shuffle and we can split the partition with the granularity of shuffle blocks. Broadcast join doesn't have shuffles.

Yeah,  thought a lot that normal SQL can't match this case.
For our production env experience, data skew (such as stream side is group by and skewed )before broadcast nested loop join always cause a  long running time.
two ways to avoid this case :

avoid nested loop join.
use distribute by to increase parallelism by dispersing data.

method 1 need to handle SQL logic, for method 2, although it will cause one more time  shuffle, it 's  narrow dependent. Nowadays， network cost is cheap and always not a  bottleneck.
After try with AQE, AQE's mode is not suitable for this case. Since it doesn't have a shuffle before BNLJ.
In our inner version,  in BroadcastNestedLoopJoinExec, after stream side executed, we will get the raw count of each partition and judge if it's skewed seriously, if skewed seriously and volume is large, repartition stream side to make stream side RDD average.
It's not very elegant but the benefits are very clear. I am not sure if community will accept this way.

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after stream side executed, we will get the raw count of each partition and judge if it's skewed seriously, if skewed seriously and volume is large, repartition stream side to make stream side RDD average.

So you add a shuffle to the stream side to stop it before the join node and get statistics?

after stream side executed, we will get the raw count of each partition and judge if it's skewed seriously, if skewed seriously and volume is large, repartition stream side to make stream side RDD average.

So you add a shuffle to the stream side to stop it before the join node and get statistics?

Yes, stop before join and get count row of each stream side partitions.  re-shuffle stream side then join.

If the user manually adds a shuffle (DISTRIBUTE BY) in the query before broadcast join, I think we can take care of the skew. Spark query optimizer should not add the extra shuffle by itself, as it's likely to cause perf regression.

Spark query optimizer should not add the extra shuffle by itself, as it's likely to cause perf regression.

With this rule, we can't handle such data skew case automatic.  With strict and reasonable conf value, extra shuffle 's cost is much less than the overhead of data skew.
Especially like broadcast join/broadcast nested loop join. if stream side executing end with a group by(There are many such business scenarios) and always data skew seriously.  Getting business people to tune each job is difficult.
For the community, what do you think about this scene

Then we need some estimation work, as the shuffle/scan node may be far away from the join node. We also need to carefully justify if the extra shuffle cost worths the skew elimination benefits.

Then we need some estimation work, as the shuffle/scan node may be far away from the join node. We also need to carefully justify if the extra shuffle cost worths the skew elimination benefits.

Yea, only when skewed very serious and  threshold is reached ,  worth  to re-shuffle data.
Hope for some advise: in current code, is there any method to estimate shuffle cost?


Mouse capture API

The pull request "Add mouse capture example"  and the recipe "Grabbing the mouse" in the Bevy cookbook both illustrate how mouse capturing is done currently. It's done using the Winit API directly (though WinitWindows), which ties these Bevy apps to using Winit's backends.
Bevy should have a mouse capture API that lets us do the same thing, but on a higher level of abstraction that isn't tied directly to Winit.
In the short term, @cart is cool with adding more properties to the existing WindowDescriptor to unblock scenarios like mouse grabbing, but in the medium term one issue is that Bevy doesn't let you set window properties on demand like you can with Winit (see comment and issue #641).

Closed by #679


Making the axum extractor more idiomatic

I noticed that the current axum extractor diverges from the official Query design: https://docs.rs/axum/0.6.13/src/axum/extract/query.rs.html#51-65
In particular, I think two things can be done to make it a bit more idiomatic:

returning a custom Rejection, allowing users to either use the supplied error handler, or accept Result<QueryString<Foo>, QueryStringRejection> and deal with it in the handler
exporting multiple distinct types for parsing type vs configuring it with a layer

What do you think of those changes? If you're happy with them, I might make a stab at a PR implementing that.

Hi @si14 ,
I agree with you on both points,
For the custom rejection part, I personally prefer to just copy and modify axum's extractors, so I wasn't sure what was more idiomatic, and I gladly would accept a PR for it.
For the parsing method part, what names do you suggest for these new extractors?


HLDS Crash with NO ERRORS

Describe the bug
I use YapB in my server, however it makes hlds stop like "hang".
No errors or logs, just that HLDS stops. I can Exit it and Start smoothly again.
Expected behavior
Smooth 24/7 not crashing HLDS.
Video
N/A
Environment details:

OS: windows 10
Engine: HLDS
GameDLL: hl.dll
Metamod: metamod
Bot Version: YapB 4.2.623
Game mode: PUB

Additionally, please provide list of AMX Mod X plugins: amxx plugins and list of Metamod plugins: meta plugins.
Currently loaded plugins:
name                    version     author            file             status
[  1] Admin Base              1.8.2       AMXX Dev Team     admin.amxx       running
[  2] Admin Commands          1.8.2       AMXX Dev Team     admincmd.amxx    running
[  3] Slots Reservation       1.8.2       AMXX Dev Team     adminslots.amxx  running
[  4] Menus Front-End         1.8.2       AMXX Dev Team     menufront.amxx   running
[  5] Commands Menu           1.8.2       AMXX Dev Team     cmdmenu.amxx     running
[  6] Players Menu            1.8.2       AMXX Dev Team     plmenu.amxx      running
[  7] Maps Menu               1.8.2       AMXX Dev Team     mapsmenu.amxx    running
[  8] Plugin Menu             1.8.2       AMXX Dev Team     pluginmenu.amxx  running
[  9] Admin Chat              1.8.2       AMXX Dev Team     adminchat.amxx   running
[ 10] Anti Flood              1.8.2       AMXX Dev Team     antiflood.amxx   running
[ 11] Admin Votes             1.8.2       AMXX Dev Team     adminvote.amxx   running
[ 12] NextMap                 1.8.2       AMXX Dev Team     nextmap.amxx     running
[ 13] TimeLeft                1.8.2       AMXX Dev Team     timeleft.amxx    running
[ 14] Pause Plugins           1.8.2       AMXX Dev Team     pausecfg.amxx    running
[ 15] Stats Configuration     1.8.2       AMXX Dev Team     statscfg.amxx    running
[ 16] Restrict Weapons        1.8.2       AMXX Dev Team     restmenu.amxx    running
[ 17] StatsX                  1.8.2       AMXX Dev Team     statsx.amxx      running
[ 18] Ultimate Sounds         1.7         Dizzy / Bmann_42  ultimate_sounds  running
[ 19] Vote Ban                1.0         Alka              voteban.amxx     running
[ 20] Admin Check             1.51        OneEyed           admin_check.amx  running
[ 21] GHW Connect Messages    1.1         GHW_Chronic       GHW_connect.amx  running
[ 22] unknown                 unknown     unknown           tunnel.amxx      running
[ 23] Autoresponder/Advertis  0.5         MaximusBrood      ad_manager.amxx  running
[ 24] Admin Model Menu        1.0         Dimision          admodelsCT.amxx  running
[ 25] Admin Model Menu        1.0         Dimision          admodelsT.amxx   running
[ 26] Admin Check             1.51        OneEyed           vip_check.amxx   running
[ 27] Auto Round Restart      1.6         SubStream         autorr.amxx      running
[ 28] Ping Faker              1.5a        MeRcyLeZZ         pingfaker.amxx   running
[ 29] Server Models           1.0         feruchio          finalweapon.amx  running
[ 30] Show Players            1.0         NapoleoN#         dailyrestart.amxx  running
[ 31] ANTI Change Name        0.1beta     F.E.A.R.&Many     nochangename.amxx  running
[ 32] botespectador           1.0         |Polimpo4|      PMN_BOT_SPEC.amxx running

Currently loaded plugins:
description      stat pend  file              vers      src  load  unlod
[ 1] AMX Mod X        RUN   -    amxmodx_mm.dll    v1.8.2    ini  Start ANY
[ 2] STATSME          RUN   -    statsme_mm.dll    v2.8.3    ini  Chlvl Chlvl
[ 3] Booster          RUN   -    booster_mm.dll    v2.40     ini  Chlvl Pause
[ 4] HLGuard          RUN   -    hlguard_mm.dll    v1.9.n10  ini  Chlvl Chlvl
[ 5] YaPB             RUN   -    yapb.dll          v4.2.623  ini  Chlvl ANY
[ 6] CStrike          RUN   -    cstrike_amxx.dll  v1.8.2     pl1  ANY   ANY
[ 7] CSX              RUN   -    csx_amxx.dll      v1.8.2    pl1  ANY   ANY
[ 8] FakeMeta         RUN   -    fakemeta_amxx.dl  v1.8.2    pl1  ANY   ANY
[ 9] Ham Sandwich     RUN   -    hamsandwich_amxx  v1.8.2    pl1  ANY   ANY
[10] Fun              RUN   -    fun_amxx.dll      v1.8.2    pl1  ANY   ANY
[11] Engine           RUN   -    engine_amxx.dll   v1.8.2    pl1  ANY   ANY
Additional context
Happening with PLAYERS connected or even WHEN NO PLAYERS are connected.
HLDS just stops with no error.
Looking forward!

Which version of metamod do you use?
I think using Metamod v1.21.1-am could be more stable than metamod-p.

https://sync.jeefo.net/u/d/7e42de8188874631b290/
you can upload here. it will be private.


Ping diagnostics tool, explicitly set IP version for IPv4

Invoking ping with a hostname without -6 or -4 gives no control over which IP version is used. From man ping(8):

When invoked with a hostname, the version to which	the target is resolved first is used.

# /sbin/ping -c '3' 'opnsense.org'
PING6(56=40+8+8 bytes) 2a02:8071:3100::xxxx --> 2001:1af8:4700:a1fa:3::2
16 bytes from 2001:1af8:4700:a1fa:3::2, icmp_seq=0 hlim=56 time=28.444 ms
16 bytes from 2001:1af8:4700:a1fa:3::2, icmp_seq=1 hlim=56 time=20.165 ms
16 bytes from 2001:1af8:4700:a1fa:3::2, icmp_seq=2 hlim=56 time=27.399 ms

--- opnsense.org ping6 statistics ---
3 packets transmitted, 3 packets received, 0.0% packet loss
round-trip min/avg/max/std-dev = 20.165/25.336/28.444/3.681 ms

good lord, the whole ping/ping6 merge in FreeBSD has been a horrible endeavour

applied manually with a small tweaks as a6ba422b2328 -- thanks!

Note: pretty sure this worked until 21.7 and FreeBSD 13 had some issues.. like this one.. https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=260314


agent: native histogram support

This PR adds support for appending standard and float native histograms to the agent DB which is needed for remote writing native histograms in agent mode.

Awesome, thanks for this! I'll have time to review this in the morning.

Thanks for the fast review @codesome!


BUG: Wrong Param Types

Due update to PHP 8.x, all class methods got their own param types declaration. In some cases, the value may not be sent in the correct format. This issue holds all fixes about this.

done.


Use npx for local browser testing

I changed the test-browser script to use npx. This prevents npm from messing up the package.json and package-lock.json when you npm run test-browser.
To be on the safe side, I copied the old version of the command to test-browser-ci for the Travis build.
@jashkenas FYI.  Please don't worry about the order, I'll fix any merge conflicts in #2826 if the need arises.

When testing on a different machine, I found out that Karma cannot reliably find PhantomJS when following this approach. It happened to work on the machine where I created this PR because I already had a global installation of PhantomJS. I'm withdrawing the PR for this reason.


If using extension of TestMethodAttribute then please contact vendor (ThreadSafeStringWriter)

Description
Parallel tests are failing sporadically if they are writing to console output.
Steps to reproduce

Create default project dotnet new mstest
Add many classes with tests
Put Console.WriteLine("abc") in tests body
Allow tests to be executed in parallel [assembly: Parallelize(Scope = ExecutionScope.ClassLevel)]
Update mstest packages to version 2.2.9

Execute all tests via dotnet test many times and sometimes different error messages appear.
Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor. Error message: An item with the same key has already been added. Key: out, Stack trace:    at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter..ctor(IFormatProvider formatProvider, String outputType)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.LogMessageListener..ctor(Boolean captureDebugTraces)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments)
   at Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

or
An exception occurred while invoking executor 'executor://mstestadapter/v2': One or more errors occurred. (An item with the same key has already been added. Key: context)
Stack trace:
   at System.Threading.Tasks.Task.WaitAllCore(Task[] tasks, Int32 millisecondsTimeout, CancellationToken cancellationToken)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTestsInSource(IEnumerable`1 tests, IRunContext runContext, IFrameworkHandle frameworkHandle, String source, Boolean isDeploymentDone)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTests(IEnumerable`1 tests, IRunContext runContext, IFrameworkHandle frameworkHandle, Boolean isDeploymentDone)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.RunTests(IEnumerable`1 sources, IRunContext runContext, IFrameworkHandle frameworkHandle, TestRunCancellationToken cancellationToken)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.MSTestExecutor.RunTests(IEnumerable`1 sources, IRunContext runContext, IFrameworkHandle frameworkHandle)
   at Microsoft.VisualStudio.TestPlatform.CrossPlatEngine.Execution.RunTestsWithSources.InvokeExecutor(LazyExtension`2 executor, Tuple`2 executorUriExtensionTuple, RunContext runContext, IFrameworkHandle frameworkHandle)
   at Microsoft.VisualStudio.TestPlatform.CrossPlatEngine.Execution.BaseRunTests.RunTestInternalWithExecutors(IEnumerable`1 executorUriExtensionMap, Int64 totalTests)

Inner exception: An item with the same key has already been added. Key: context

Stack trace:
   at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter..ctor(IFormatProvider formatProvider, String outputType)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.UnitTestRunner.RunSingleTest(TestMethod testMethod, IDictionary`2 testContextProperties)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTestsWithTestRunner(IEnumerable`1 tests, IRunContext runContext, ITestExecutionRecorder testExecutionRecorder, String source, IDictionary`2 sourceLevelParameters, UnitTestRunner testRunner)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.<>c__DisplayClass17_1.<ExecuteTestsInSource>b__6()
   at System.Threading.Tasks.Task.InnerInvoke()
   at System.Threading.Tasks.Task.<>c.<.cctor>b__272_0(Object obj)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state)
--- End of stack trace from previous location ---
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot, Thread threadPoolThread)

or
 An item with the same key has already been added. Key: err
  Stack Trace:
     at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter..ctor(IFormatProvider formatProvider, String outputType)

or
 Operations that change non-concurrent collections must have exclusive access. A concurrent update was performed on this collection and corrupted its state. The collection's state is no longer correct.
  Stack Trace:
     at System.Collections.Generic.Dictionary`2.Remove(TKey key)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.Dispose(Boolean disposing)
   at System.IO.TextWriter.Dispose()

Everything is related to MSTestAdapter.PlatformServices.ThreadSafeStringWriter.
Versions
<PackageReference Include="MSTest.TestAdapter" Version="2.2.9" />
<PackageReference Include="MSTest.TestFramework" Version="2.2.9" />

Also reproducible in 2.2.8.

Hi, this is happening for me also. My case is much different than @nvborisenko 's, but still the same results.

Everything worked great in 2.2.8, failures started when I moved to 2.2.9.
My tests do not run in parallel.
Failing tests don't write to console

Running the tests several times in a row in Azure Dev Ops or GitHub Actions produces a different failure profile every time. Same error message, different combinations of tests.
I will work on a focused repro. In the meantime, I can point to a public github repo where it's failing, if that would help.
Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor.
Error message: Index was out of range. Must be non-negative and less than the size of the collection. (Parameter 'chunkLength'), Stack trace: at System.Text.StringBuilder.ToString() at
Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.ToStringAndClear() at
Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments) at
Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod) at
Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

Same issue for me, I upgraded to 2.2.9 yesterday. And I've started seeing intermittent issues running tests - in my case using the DataTestMethod attribute (probably because they run faster than my other tests). Rerunning the failing tests individually shows they pass.
    Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor. Error message: Index was out of range. Must be non-negative and less than the size of the collection. (Parameter 'chunkLength'), Stack trace:    at System.Text.StringBuilder.ToString()
       at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.ToStringAndClear()
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.LogMessageListener.GetAndClearStandardOutput()
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments)
       at Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod)
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

Variation of stack trace:
    Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor. Error message: Index was out of range. Must be non-negative and less than the size of the collection. (Parameter 'chunkLength'), Stack trace:    at System.Text.StringBuilder.ToString()
       at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.ToStringAndClear()
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.LogMessageListener.GetAndClearStandardOutput()
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments)
       at Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod)
       at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

I created a 100% reliable repro for this issue here: https://github.com/jcoliz/testfx-issue1077.
I did need to parallelize the test in order to get it to reliably fail. Although in my own case, there's no parallelism.
It fails with many different call stacks
System.IndexOutOfRangeException: Index was outside the bounds of the array.
  Stack Trace:
      at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.WriteLine(String value)
   at System.IO.TextWriter.WriteLine(String format, Object arg0)
   at System.IO.TextWriter.SyncTextWriter.WriteLine(String format, Object arg0)
   at System.Console.WriteLine(String format, Object arg0)

   Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor. Error message: Index was out of range. Must be non-negative and less than the size of the collection. (Parameter 'chunkLength'), Stack trace:    at System.Text.StringBuilder.ToString()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.ToStringAndClear()
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.LogMessageListener.GetAndClearStandardOutput()
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments)
   at Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

Inner exception: Index was outside the bounds of the array.

Stack trace:
   at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter..ctor(IFormatProvider formatProvider, String outputType)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.UnitTestRunner.RunSingleTest(TestMethod testMethod, IDictionary`2 testContextProperties)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTestsWithTestRunner(IEnumerable`1 tests, IRunContext runContext, ITestExecutionRecorder testExecutionRecorder, String source, IDictionary`2 sourceLevelParameters, UnitTestRunner testRunner)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.<>c__DisplayClass17_1.<ExecuteTestsInSource>b__6()
   at System.Threading.Tasks.Task.InnerInvoke()
   at System.Threading.Tasks.Task.<>c.<.cctor>b__272_0(Object obj)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state)
--- End of stack trace from previous location ---
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Threading.Tasks.Task.ExecuteWithThreadLocal(Task& currentTaskSlot, Thread threadPoolThread)

An exception occurred while invoking executor 'executor://mstestadapter/v2': One or more errors occurred. (Index was outside the bounds of the array.) (An item with the same key has already been added. Key: context)
Stack trace:
   at System.Threading.Tasks.Task.WaitAllCore(Task[] tasks, Int32 millisecondsTimeout, CancellationToken cancellationToken)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTestsInSource(IEnumerable`1 tests, IRunContext runContext, IFrameworkHandle frameworkHandle, String source, Boolean isDeploymentDone)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.ExecuteTests(IEnumerable`1 tests, IRunContext runContext, IFrameworkHandle frameworkHandle, Boolean isDeploymentDone)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestExecutionManager.RunTests(IEnumerable`1 sources, IRunContext runContext, IFrameworkHandle frameworkHandle, TestRunCancellationToken cancellationToken)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.MSTestExecutor.RunTests(IEnumerable`1 sources, IRunContext runContext, IFrameworkHandle frameworkHandle)
   at Microsoft.VisualStudio.TestPlatform.CrossPlatEngine.Execution.RunTestsWithSources.InvokeExecutor(LazyExtension`2 executor, Tuple`2 executorUriExtensionTuple, RunContext runContext, IFrameworkHandle frameworkHandle)
   at Microsoft.VisualStudio.TestPlatform.CrossPlatEngine.Execution.BaseRunTests.RunTestInternalWithExecutors(IEnumerable`1 executorUriExtensionMap, Int64 totalTests)

   Exception thrown while executing test. If using extension of TestMethodAttribute then please contact vendor. Error message: Index was outside the bounds of the array., Stack trace:    at System.Collections.Generic.Dictionary`2.TryInsert(TKey key, TValue value, InsertionBehavior behavior)
   at System.Collections.Generic.Dictionary`2.Add(TKey key, TValue value)
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter.GetOrAddStringBuilder()
   at Microsoft.VisualStudio.TestPlatform.MSTestAdapter.PlatformServices.ThreadSafeStringWriter..ctor(IFormatProvider formatProvider, String outputType)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.LogMessageListener..ctor(Boolean captureDebugTraces)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodInfo.Invoke(Object[] arguments)
   at Microsoft.VisualStudio.TestTools.UnitTesting.TestMethodAttribute.Execute(ITestMethod testMethod)
   at Microsoft.VisualStudio.TestPlatform.MSTest.TestAdapter.Execution.TestMethodRunner.ExecuteTest(TestMethodInfo testMethodInfo)

Thank you for the report, we are working on a fix, I'll released a preview couple of days ago, could you try 2.2.10-preview-20220414-01 version of MSTest and see if the issue repros?

Verified on 2.2.10-preview-20220414-01, the issue went away.

@nvborisenko thank you for the verification!

@Haplois Confirmed here as well. Both on my actual use case and on the synthetic repro.


Update README.md - Modules

Examples and explanations for the module system

Looking good! I'll revise this PR a bit (e.g. mention how modules are just
records) and merge it tomorrow. Thanks!
On Sat, Aug 21, 2021, 21:29 mathis2003 @.***> wrote:

Examples and explanations for the module system
You can view, comment on, or merge this pull request online at:
https://github.com/vrtbl/passerine/pull/58
Commit Summary

Update README.md

File Changes

M README.md
https://github.com/vrtbl/passerine/pull/58/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5
(48)

Patch Links:

https://github.com/vrtbl/passerine/pull/58.patch
https://github.com/vrtbl/passerine/pull/58.diff

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[pegtl] Update 3.0.0-pre to most recent commit

Update the PEGTL 3.0.0-pre port to the most recent commit on master from 1/25/2020.

What does your PR fix? Fixes issue #

PEGTL hasn't released version 3.0.0 yet, but there have been plenty of commits since the last update to this port which are moving it forward.

Which triplets are supported/not supported? Have you updated the CI baseline?

Should be all of them.

Does your PR follow the maintainer guide?

Yes.

LGTM! Thanks @wravery :)


TagBot trigger issue

This issue is used to trigger TagBot; feel free to unsubscribe.
If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.
If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Triggering TagBot for merged registry pull request: https://github.com/JuliaRegistries/General/pull/86849

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This extra notification is being sent because I expected a tag to exist by now, but it doesn't.
You may want to check your TagBot configuration to ensure that it's running, and if it is, check the logs to make sure that there are no errors.

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Support for ScyllaDB

Support for ScyllaDB
Read about Authorizer support for Cassandra #126 .
Which should make it also compatible with ScyllaDB Open Source.
Validate Compatibility; Add to README
Would love it if you could validate Authorizer works with ScyllaDB Open Source, and we can recommend it as a solution to our user base.
Alternatives
ScyllaDB also has commercial Enterprise and DBaaS offerings; we'd presume those would also work once testing was complete on open source.

@PeterCorless thank you for the great suggestion will perform testing and let you know the results

@PeterCorless all the integration tests are passing for Scylla DB and also did the basic manual testing :-)
I have tested with the OSS docker version
version: '3.9'

services:
  db:
    container_name: scylla
    image: scylladb/scylla
    ports:
      - 9042:9042

Is there any specific things that I should be aware for the cloud version?

@PeterCorless getting some error with cloud version
I followed instructions given on connect section

package main

import (
    "fmt"
    "github.com/gocql/gocql"
)

func main() {
    var cluster = gocql.NewCluster("<IP_ADDRESS>", "<IP_ADDRESS>", "<IP_ADDRESS>")
    cluster.Authenticator = gocql.PasswordAuthenticator{Username: "scylla", Password: "***************"}
    cluster.PoolConfig.HostSelectionPolicy = gocql.DCAwareRoundRobinPolicy("AWS_US_EAST_1")

    var session, err = cluster.CreateSession()
    if err != nil {
        panic("Failed to connect to cluster")
    }
}

It should work exactly the same. It look like you don't have connectivity to the cluster IP addresses.

@avikivity i tried with default ip detection that scylladb dashboard does.
Though will try it again and let you know

@avikivity I tried one more time, still getting the same error.
I also verified my IP address it is whitelisted correctly.

I can't help on this bug tracker, it's a connectivity problem that happens before you ever reach Scylla. Try the #cloud channel in https://slack.scylladb.com.

@PeterCorless I have added support for ScyllaDB, it would be great if you can spread the word in the community thanks.


Cannot disable completion for a specified client

I use a language server for which I want to disable the most of capabilities (it's too slow on some projects). Currently it does not disable any capability given restricted set of capabilities on initialization.
I noticed that restricting client.resolved_capabilities within on_attach can also prevent from using some method of client but completion is an exception.
Shouldn't source:is_available() return false if self.client.resolved_capabilities.completion is false?

You cannot use the config?
https://github.com/hrsh7th/nvim-cmp/issues/822#issuecomment-1056103013
If so, it is the LSP problem instead of nvim-cmp.
LSP server must support the capability.

Thanks, however I've seen before in source:is_available() that overriding server_capabilities.completionProvider can be another workaround (and works).
In general, what is "the proper way" to override the server capabilities (i.e. whether not checking resolved_capabilities.completion is correct)?
https://github.com/neovim/neovim/blob/a7c999523dbcbb91db56c6eb834034d448e9481c/runtime/lua/vim/lsp.lua#L1469-L1474
https://github.com/neovim/neovim/blob/a7c999523dbcbb91db56c6eb834034d448e9481c/runtime/lua/vim/lsp.lua#L966-L974
Independently, I have no doubt that this is a server problem in particular :wink:

See :h cmp-nvim-lsp


clean up CREATE ASYMMETRIC KEY

These changes pertain to Issue #2198 .

Syntax section:

Lowercased user-supplied values to be consistent with other documentation pages

Arguments section:

Added missing entry for asym_key_name
Moved AUTHORIZATION to the top to match order in Syntax section
Improved definition of FILE option
Improved definition of EXECUTABLE FILE option
Improved definition of ASSEMBLY option
Added missing entry for PROVIDER
Removed ENCRYPTION BY *\<key_name_in_provider>* as it is not a valid as stated (is part of ENCRYPTION BY PASSWORD -- see below)
Moved ALGORITHM up to match order of options shown in Syntax section
Changed PASSWORD to be ENCRYPTION BY PASSWORD
Lowercased user-supplied values to be consistent with other documentation pages

Remarks section:

Added "or DLL file" to end of 1st paragraph, regarding the FROM clause (yes, DLL from either file system or as a loaded assembly -- same thing just different location -- only stores the public key)

Removed 3rd sentence of 2nd paragraph -- "If a database master key does exist, the password is optional." -- as it contradicted the 2nd sentence, and was just incorrect. With no DMK, the following statement:
CREATE ASYMMETRIC KEY [AKeyNoPassword]
WITH ALGORITHM = RSA_2048;

gets the following error:

/*
Msg 15581, Level 16, State 6, Line XXXXX
Please create a master key in the database or open the master key in the session before performing this operation.
*/

Examples section:

In example "B", for correctness changed

and then authorizes user Christina to use the asymmetric key

to be:

and assigns ownership of the asymmetric key to user Christina

In example "B", for variety removed ENCRYPTION BY PASSWORD clause as that is shown in example "A". Without this clause, the Database Master Key will be used, hence it must already exist. I added a sentence mentioning this to the end of the example description.

In example "C", for correctness changed

stored in a file. It then encrypts it using an Extensible

to be:

stored in an Extensible

In example "C", fixed name "EKMProvider1" to be "EKM_Provider1" (to match T-SQL statement) in example description

In example "C", not sure if lack of ENCRYPTION BY PASSWORD implies Database Master Key is used, or if that is a non-issue when using an EKM provider. I have never used an EKM provider so for now I am leaving that part as is (i.e. not mentioned in the example description).

See Also section:

Moved "Choose an Encryption Algorithm" to below statements and functions for better organization
Added links to functions: ASYMKEYPROPERTY and ASYMKEY_ID

@srutzky : Thanks for your contribution! The author, @VanMSFT, has been notified to review your proposed change.

@srutzky - The changes look great! Thank you so much for your efforts. We really appreciate it.
Reviewed. #sign-off

manually added the 'ready-to-merge' label...
@VanMSFT - can you check that the relative links are working after this is live? I've reviewed them and they appear to be good, but without staging tools, they should be double-checked after the changes have bee published.  Thanks.

Verified links worked. Thanks all!


Remove hypr login page from identity-apps

Describe the issue:

Hypr login page has been migrated to identity-apps in the unification effort, but it shouldn't be present there as the hypr login page should come with the hypr connector.
Since the connector documentation instructs to copy the jsp page from connector to identity-apps [1], having the jsp page in the identity-apps itself by default can cause confusions to the end users.
However, since we provide hypr connector OOTB in asgardeo, we need to include the file in the cloud-extensions.
[1] https://github.com/wso2-extensions/identity-outbound-auth-hypr/blob/main/docs/config.md#:~:text=Step 4%3A Deploying the HYPR login page
How to reproduce:
N/A
Expected behavior:

N/A
Environment information (Please complete the following information; remove  any unnecessary fields) :

Product Version: [e.g., IS 5.10.0, IS 5.9.0] N/A
OS: [e.g., Windows, Linux, Mac] N/A
Database: [e.g., MySQL, H2] N/A
Userstore: [e.g., LDAP, JDBC] N/A

Optional Fields
Related issues:

Suggested labels:

The same issue will arise with the iproovlogin.jsp as well. For Identity Server iProov will be integrated as a connector which is available in the connector store whereas for Asgardeo iProov will be a default connection.


Implement mol_id for the loaders

Optionally include the molecule ID to facilitate analysis

[x] Implement mol_id:

[x] Ace
[x] ANI family
[x] COMP6 family
[x] QM9q
[x] SPICE

@stefdoerr could you review?

Yes, I'm reusing these loaders (https://github.com/Acellera/AceForce/pull/12)


需要自定义电话登录逻辑，以及自定义电话字段格式

需要自定义电话登录逻辑，以及自定义电话字段格式

The nhost team speaks many languages but I am afraid Chinese isn't amongst them. Would you mind explaining your issue in english?
Thanks!

I have some questions, such as how to customize the SMS login logic, I want to implement my own SMS verification code, and customize the phone number format. How to use third-party storage systems, such as Alibaba Cloud OSS. How to add interceptors for dynamically modifying logic, such as temporarily adding a keyword filtering system to filter keywords in advance when posting comments.
@dbarrosop

And how to monitor data changes, such as how to inform users when someone comments.
@dbarrosop

If you have questions I'd suggest opening different topics under discussions, preferably one per question so it's easier to deal with. Issues are mostly for bug reports.
I am closing this issue as this is not a bug report but, please, start discussions with your questions so we can discuss them.


Fix Indy SDK AnonCreds test

I noticed that one of the hardest tests to get passed in the CI is indy-sdk-anoncreds-registry.e2e.test.ts . It usually throws something like:
expect(received).toMatchObject(expected)

    - Expected  - 21
    + Received  +  1

      Object {
    -   "credentialDefinition": Object {
    -     "issuerId": "TL1EaPFCZ8Si5aUrqScBDt",
    -     "schemaId": "TL1EaPFCZ8Si5aUrqScBDt:2:test - 11:1.58.150614981316885",
    -     "tag": "TAG",
    -     "type": "CL",
    -     "value": Object {
    -       "primary": Object {
    -         "n": "...",
    -         "r": Object {
    -           "age": "...",
    -           "master_secret": "57770757113548032970308439965749734[1334](https://github.com/hyperledger/aries-framework-javascript/actions/runs/4253131974/jobs/7399528837#step:10:1335)...",
    -         },
    -         "rctxt": "...",
    -         "s": "...",
    -         "z": "18569464356833363098514177097771727[1339](https://github.com/hyperledger/aries-framework-javascript/actions/runs/4253131974/jobs/7399528837#step:10:1340)...[1344](https://github.com/hyperledger/aries-framework-javascript/actions/runs/4253131974/jobs/7399528837#step:10:1345)...",
    -       },
    -     },
    -   },
        "credentialDefinitionId": "TL1EaPFCZ8Si5aUrqScBDt:3:CL:33:TAG",
    -   "credentialDefinitionMetadata": Object {
    -     "didIndyNamespace": "pool:localtest",
    -   },
    +   "credentialDefinitionMetadata": Object {},
        "resolutionMetadata": Object {},
      }

      145 |     )
      146 |
    > 147 |     expect(credentialDefinitionResponse).toMatchObject({
          |                                          ^
      148 |       credentialDefinitionId: `TL1EaPFCZ8Si5aUrqScBDt:3:CL:${schemaResponse.schemaMetadata.indyLedgerSeqNo}:TAG`,
      149 |       credentialDefinition: {
      150 |         issuerId: 'TL1EaPFCZ8Si5aUrqScBDt',

      at Object.<anonymous> (tests/indy-sdk-anoncreds-registry.e2e.test.ts:147:42)

I remember that in some former Indy SDK ledger tests there were some sleep(xxx) due to the amount of time it takes for the ledger to actually settle the value. Could this be also the case?

Ah good shout. Yes I think that could be the case here. It fails way more often in CI, probably because it's slow....


fonttools: 3.0 -> 3.13.0

Motivation for this change
version bump
Things done

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

[x] NixOS
[ ] macOS
[ ] Linux

[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
[ ] Tested execution of all binary files (usually in ./result/bin/)
[x] Fits CONTRIBUTING.md.

Can you move the expression to pkgs/development/python-modules/fonttools/default.nix?
Besides, looks good to me.

Done.


Update launch.json

VSCode no longer accepts relative paths so ${workspaceRoot} needs added to outDir

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Examples are out of date

The script referenced in the examples/host-guest example README is wrong. It should be prepare_host_guest.py.

Not sure if this an issue with my setup but I seem to get TypeError and ValueError in the examples/Atom-mapping.ipynb Jupyter Notebook when trying:
from perses.utils.smallmolecules import render_atom_mapping

(Using openeye-toolkits version 2019.10.2)
Here is the full error output:
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/amber.py in find_gaff_dat()
    272         try:
--> 273             AMBERHOME = os.path.split(full_path)[0]
    274             AMBERHOME = os.path.join(AMBERHOME, "../")

~/opt/anaconda3/envs/perses/lib/python3.6/posixpath.py in split(p)
    106     everything after the final slash.  Either part may be empty."""
--> 107     p = os.fspath(p)
    108     sep = _get_sep(p)

TypeError: expected str, bytes or os.PathLike object, not NoneType

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
<ipython-input-1-186b929aa616> in <module>
      1 # from perses.utils.openeye import createOEMolFromSDF
----> 2 from perses.utils.smallmolecules import render_atom_mapping
      3 from perses.utils.openeye import smiles_to_oemol
      4 from perses.rjmc.topology_proposal import AtomMapper
      5 from openeye import oechem

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/perses-0.6.0.dev0-py3.6.egg/perses/utils/__init__.py in <module>
      1 from perses.utils.data import *
----> 2 from perses.utils.openeye import *

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/perses-0.6.0.dev0-py3.6.egg/perses/utils/openeye.py in <module>
      9
     10 from openeye import oechem, oegraphsim
---> 11 from openmoltools.openeye import generate_conformers
     12 from simtk import openmm, unit
     13 from simtk.openmm import app

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/__init__.py in <module>
     24 """
     25
---> 26 from openmoltools import amber_parser, system_checker, utils, packmol, openeye, amber, cirpy, gromacs, schrodinger

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/openeye.py in <module>
      3 import mdtraj as md
      4 from openmoltools.utils import import_, enter_temp_directory, create_ffxml_file
----> 5 from openmoltools.amber import run_antechamber
      6 import logging
      7

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/amber.py in <module>
    281     return os.path.join(AMBERHOME, 'dat', 'leap', 'parm', 'gaff.dat')
    282
--> 283 GAFF_DAT_FILENAME = find_gaff_dat()
    284
    285

~/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/amber.py in find_gaff_dat()
    274             AMBERHOME = os.path.join(AMBERHOME, "../")
    275         except:
--> 276             raise(ValueError("Cannot find AMBER GAFF"))
    277
    278     if AMBERHOME is None:

ValueError: Cannot find AMBER GAFF

In the cdk2 example, repex appears to work! An error is raised when using sams or nonequlibrium. Also,  the cdk2_sams.yaml references to the wrong protein and ligand file.
Error message
2020-06-03 12:36:30,558:(2.72s):relative_setup:	preparing to add solvent Traceback (most recent call last):   File "/home/david/miniconda2/envs/perses/bin/perses-relative", line 8, in <module>     sys.exit(run())   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/perses/app/setup_relative_calculation.py", line 623, in run     setup_dict = run_setup(setup_options)   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/perses/app/setup_relative_calculation.py", line 380, in run_setup     trajectory_directory=trajectory_directory, trajectory_prefix=setup_options['trajectory_prefix'], nonbonded_method=setup_options['nonbonded_method'])   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/perses/app/relative_setup.py", line 284, in __init__     self._complex_topology_old, self._complex_positions_old,phase='complex')   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/perses/app/relative_setup.py", line 666, in _solvate_system     modeller.addSolvent(self._system_generator.forcefield, model=model, padding=self._padding, ionicStrength=0.15*unit.molar)   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/simtk/openmm/app/modeller.py", line 485, in addSolvent     system = forcefield.createSystem(self.topology)   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 1164, in createSystem     if generator(self, res):   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/openmmforcefields/generators/template_generators.py", line 528, in generator     forcefield.loadFile(self.gaff_xml_filename)   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 256, in loadFile     self.registerAtomType(type.attrib)   File "/home/david/miniconda2/envs/perses/lib/python3.7/site-packages/simtk/openmm/app/forcefield.py", line 390, in registerAtomType     raise ValueError('Found multiple definitions for atom type: '+name) ValueError: Found multiple definitions for atom type: c

@schallerdavid - CDK2 has some weird phospho-residue in it called TPO! It needs the forcefield files like this:
forcefield_files:
    - amber/ff14SB.xml # ff14SB protein force field
    - amber/tip3p_standard.xml # TIP3P and recommended monovalent ion parameters
    - amber/tip3p_HFE_multivalent.xml # for divalent ions
    - amber/phosaa10.xml # HANDLES THE TPO

Where phosaa10.xml is the important bit. I hadn't changed this in sams or nonequilibrium yaml file before, but I have now! And I've fixed the protein/ligand filenames too for sams!

@WG150
hmmm can you just try antechamber and see that you've got it installed? Also could you do
conda list openmoltools please?

I think that in examples/cdk2-example/ the trajectory_directory in the cdk2_repex.yaml file name needs to be changed to cdk2_repex_hbonds.

@WG150 would you be happy to make that fix in the fix-examples branch?

In the Jupyter Notebook Atom-mapping.ipynb (/examples/atom-mapping) the .sdf file that molecules = Molecule.from_file('Bace_ligands_shifted.sdf') is loading is not in the working directory.

For all python scripts in examples/dualtopology I recieve an error when importing the dualtopology module:
Traceback (most recent call last):
  File "amino_acid_example.py", line 1, in <module>
    from perses import dualtopology
ImportError: cannot import name 'dualtopology'

Ok I have no idea what dualtopology does so I've gotten rid of it, it was 5 years old and we can't do dual topology in perses...
I've fixed Atom-mapping.ipynb! There is now a wget inside the notebook so it's a bit tidier, its a good script to play with to understand how we do single topology, looking at oechem.oexpropts:
https://docs.eyesopen.com/toolkits/python/oechemtk/OEChemConstants/OEExprOpts.html
Maybe try with a few other molecules too to see what's good

The README in examples/freesolv needs to be more descriptive. There are python scripts in the directory that are not referenced and it is unclear where to start. Also the bash script referenced in the README (prepare_freesolv.sh) references mols2pdf.py and molgrep.py scripts that don't exist.

example/host-guest is missing the setup_relative_calculation.py script described in the README.

In examples/neq-switching/run_equilibrium_setup.py there is an import error at:
from perses.rjmc.topology_proposal import TopologyProposal, SystemGenerator

It looks like SystemGenerator should be ProposalEngine now?

Ah we now use the SystemGenerator from openmmforcefields
from openmmforcefields.generators import SystemGenerator

Ah we now use the SystemGenerator from openmmforcefields
from openmmforcefields.generators import SystemGenerator

I've now addressed this in #683.
At the end of the script it also seems that AtomMapper is being used but not imported anywhere:
atom_mapper = AtomMapper(mol_list)

examples/relay-example needs documentation.

I'm getting a weird error in examples/rjmc/run_example.py at line 38 in oemol_to_openmm_system:
prmtop_file, inpcrd_file = openmoltools.utils.run_tleap(molecule_name, gaff_mol2, frcmod)
    prmtop = app.AmberPrmtopFile(prmtop_file)

I get the error:
Unexpected errors encountered running AMBER tool. Offending output:
Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.
Traceback (most recent call last):
  File "run_example.py", line 211, in <module>
    run()
  File "run_example.py", line 66, in run
    initial_molecule, "ligand_old"
  File "run_example.py", line 51, in oemol_to_openmm_system
    molecule_name, gaff_mol2, frcmod
  File "/Users/williamglass/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/amber.py", line 465, in run_tleap
    check_for_errors( output, other_errors = ['Improper number of arguments'] )
  File "/Users/williamglass/opt/anaconda3/envs/perses/lib/python3.6/site-packages/openmoltools/amber.py", line 257, in check_for_errors
    raise(RuntimeError("Error encountered running AMBER tool. Exiting."))
RuntimeError: Error encountered running AMBER tool. Exiting.

After looking up openmoltools.amber.run_tleap it seems this usage is ok (i.e. correct number of arguments)... any idea what's causing this error?

What ambertools is installed in the environment? Do you have access to the tleap logs? They should be somewhere in the temporary directory.

Could you try use this function instead?
https://github.com/choderalab/perses/blob/bf6fa5463521a0376d1afe0e22a6ea1e4ab5ee07/perses/utils/openeye.py#L202

I think we made good progress on this, so closing for now


[Subtitles] stop on very long video

I downloaded a 6 hour python course from YT and after a 5:05 hour mark, the subtitle file ended.
Reproduce it:
 youtube-dl --write-sub --write-auto-sub --skip-download --id _uQrJ0TkZlc
the generated VTT file will end, even though there is 1 more hour of video
the vtt file has 13594 lines and is 406438B

If playing the video in the browser, the subtitles also end at the same time. So I guess the subtitle isn't complete on YT side either. Not much ytdl could to there I guess.
https://youtu.be/_uQrJ0TkZlc?t=18290

If playing the video in the browser, the subtitles also end at the same time. So I guess the subtitle isn't complete on YT side either. Not much ytdl could to there I guess.
https://youtu.be/_uQrJ0TkZlc?t=18290

Closed


Implement linting checks

Lints can be run with hack/lint-python-code.sh.  We now check for a few things:

pep8 consistency
code complexity
code maintainability
dead code
common errors

This also reformats the python step definitions to be in compliance with these checks.
Signed-off-by: Andy Sadler<EMAIL_ADDRESS>

No objection, but I don't know enough to judge.


Best practice for catch all route?

Hi, thanks for your efforts with this repo.
Seem really solid!
If I want to catch all routes, especially those that doesn't match specified routes, what's the best way to go about it?
Thanks in advance, Anton

Hi @antonmyrberg, thank you!
In that case, I would create a regex to do it. At the moment, routes only support to match specified routes, not ignore them. A regex will do the trick.
Cheers!


code sample and name

:warning: This is a Pull Request Template :warning:

Checkout all the things you've done by placing an x within the square braces below.

Proposed Changes

[x] I've read the CODE OF CONDUCT and abide to it.
[x] I've read the CONTRIBUTING.md
[x] I've forked the repository.
[x] I've created a branch and made my changes in it.
[x] I understand opening a PULL REQUEST doesn't mean it will be merged for sure.

Contribution for Hacktoberfest 2018: Starter Edition


Names of mount points instead of device names.

Currently, devices names are used in the disks widget. It would be great if we could (maybe optionally with a mountpoints: yes flag) see the mountpoints instead of the -- sometimes not so descriptive -- device names.
Filesystems                      Size  Used  Free  Use%
  /dev/sda1                      497M  218M  279M   44%
  [===================================================]
  /dev/mapper/rootvg-rootlv      7.0G  3.0G  4.0G   43%
  [===================================================]
  /dev/mapper/rootvg-homelv      2.0G   34M  2.0G    2%
  [===================================================]
  /dev/mapper/rootvg-tmplv       1.0G   33M  1.0G    4%
  [===================================================]
  /dev/mapper/rootvg-varlv       4.0G  1.1G  2.9G   27%
  [===================================================]

It's fairly simple to find the mount point for a device:
$ findmnt --first-only --noheadings --notruncate  /dev/mapper/rootvg-varlv  | awk '{print $1}'
If nothing is returned, the device might not be mounted, so just print the device name.
In my case that would result in the much more readable:
Filesystems                      Size  Used  Free  Use%
  /boot      497M  218M  279M   44%
  [===================================================]
  /          7.0G  3.0G  4.0G   43%
  [===================================================]
  /home      2.0G   34M  2.0G    2%
  [===================================================]
  /tmp       1.0G   33M  1.0G    4%
  [===================================================]
  /var       4.0G  1.1G  2.9G   27%
  [===================================================]

@otherguy Sorry taking so long to address this. I liked the idea!
Question: I'm thinking about assuming any path lacking a /dev prefix as a mountpoint. Do you think that's safe?
Also, I'm inclined to parse /proc/mounts over relying on findmnt. Would that work in your case?

Don't worry @victorgama -- it was Christmas after all 🎄🙂
Sure, parsing /proc/mounts´ is fine, but I believe the mountpackage *always* comes withfindmnt`, giving you an easier to use and consistent interface.

@otherguy Hey there! Sorry for the delay, I was overwhelmed at work.
Would you mind sharing the content of your /proc/mounts?
In the meantime I'll run a few tests to compare how long would it take to parse /proc/mounts over calling findmnt. Wouldn't like to add extra milliseconds between connecting to a server and being able to use the shell. 🤔

@victorgama no problem, I was too ;)
Here's an example:
$ cat /proc/mounts
sysfs /sys sysfs rw,nosuid,nodev,noexec,relatime 0 0
proc /proc proc rw,relatime 0 0
udev /dev devtmpfs rw,nosuid,relatime,size=16383932k,nr_inodes=4095983,mode=755 0 0
devpts /dev/pts devpts rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000 0 0
tmpfs /run tmpfs rw,nosuid,noexec,relatime,size=3280624k,mode=755 0 0
/dev/md2 / ext4 rw,relatime,data=ordered 0 0
securityfs /sys/kernel/security securityfs rw,nosuid,nodev,noexec,relatime 0 0
tmpfs /dev/shm tmpfs rw,nosuid,nodev 0 0
tmpfs /run/lock tmpfs rw,nosuid,nodev,noexec,relatime,size=5120k 0 0
tmpfs /sys/fs/cgroup tmpfs ro,nosuid,nodev,noexec,mode=755 0 0
cgroup /sys/fs/cgroup/systemd cgroup rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgroups-agent,name=systemd 0 0
pstore /sys/fs/pstore pstore rw,nosuid,nodev,noexec,relatime 0 0
cgroup /sys/fs/cgroup/cpu,cpuacct cgroup rw,nosuid,nodev,noexec,relatime,cpu,cpuacct 0 0
cgroup /sys/fs/cgroup/blkio cgroup rw,nosuid,nodev,noexec,relatime,blkio 0 0
cgroup /sys/fs/cgroup/hugetlb cgroup rw,nosuid,nodev,noexec,relatime,hugetlb,release_agent=/run/cgmanager/agents/cgm-release-agent.hugetlb 0 0
cgroup /sys/fs/cgroup/net_cls,net_prio cgroup rw,nosuid,nodev,noexec,relatime,net_cls,net_prio 0 0
cgroup /sys/fs/cgroup/cpuset cgroup rw,nosuid,nodev,noexec,relatime,cpuset,clone_children 0 0
cgroup /sys/fs/cgroup/perf_event cgroup rw,nosuid,nodev,noexec,relatime,perf_event,release_agent=/run/cgmanager/agents/cgm-release-agent.perf_event 0 0
cgroup /sys/fs/cgroup/memory cgroup rw,nosuid,nodev,noexec,relatime,memory 0 0
cgroup /sys/fs/cgroup/pids cgroup rw,nosuid,nodev,noexec,relatime,pids,release_agent=/run/cgmanager/agents/cgm-release-agent.pids 0 0
cgroup /sys/fs/cgroup/devices cgroup rw,nosuid,nodev,noexec,relatime,devices 0 0
cgroup /sys/fs/cgroup/freezer cgroup rw,nosuid,nodev,noexec,relatime,freezer 0 0
systemd-1 /proc/sys/fs/binfmt_misc autofs rw,relatime,fd=32,pgrp=1,timeout=0,minproto=5,maxproto=5,direct 0 0
mqueue /dev/mqueue mqueue rw,relatime 0 0
hugetlbfs /dev/hugepages hugetlbfs rw,relatime 0 0
debugfs /sys/kernel/debug debugfs rw,relatime 0 0
fusectl /sys/fs/fuse/connections fusectl rw,relatime 0 0
tracefs /sys/kernel/debug/tracing tracefs rw,relatime 0 0
/dev/md1 /boot ext3 rw,relatime,data=ordered 0 0
cgmfs /run/cgmanager/fs tmpfs rw,relatime,size=100k,mode=755 0 0
none /var/lib/docker/aufs/mnt/48cf62afe205c948b63918a00d3aff19214bd8d6d7af3186f2bd290bcbc519c9 aufs rw,relatime,si=29428cccb5698340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/5c64a70a769e1c22fcaa428673acedff9b5112916201c732bbc4dcaeb97f2ea8 aufs rw,relatime,si=29428ccc17078340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/c5848d27cdfc96bea46df946e554c24df573a8a628de7ea2a0d0956a551000f5 aufs rw,relatime,si=29428cccb569a340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/2d97f8da5a7e9595d038fe7315ad2cac2a08c90e90188a8a3de91ffbe79e14f5 aufs rw,relatime,si=29428ccf38d05340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/b32c68bf5601939b9a3a3a3b76cda52ee0ddd00c25b760be4bbbef9159469f3d aufs rw,relatime,si=29428ccd5dec5340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/c1cb512e881b33aeddd1f82eee3e07d9f78c85544ab0ae661202e2c33756c37a aufs rw,relatime,si=29428ccd5dec1340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/586b98627c77b4cc8684c0816108fdc6be1ae0cd8836cc7d550ab22df8e60b17 aufs rw,relatime,si=29428cc9ad022340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/710a9b8376aa8b410da35455df3f974236d911476b50544662683aff8e6f9f53 aufs rw,relatime,si=29428ccee0ff0340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/4aadb091939f80318e098fa36f598d90e903165f9a5b5c370ed1a1549a41674b aufs rw,relatime,si=29428ccc1700f340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/892ff46ab364a2c30c62ac64c85336afccbddddec952f9bbc28d539b4c9db967 aufs rw,relatime,si=29428ccc17009340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/45192eae2f13f331bfc5c61fa242e69fb7852eab5cb577ddc9e0ad9811fee779 aufs rw,relatime,si=29428cce8ab9e340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/998011f592cbda9c32e1fba9feb8f955a43f6539e8a89f3ed83bce9f4246a0c2 aufs rw,relatime,si=29428cce8ab9a340,dio,dirperm1 0 0
none /var/lib/docker/aufs/mnt/d5c4b6d03faf1ef85a0153b09b08220a78bcb618513f4ed26b33d5ccbe18bd67 aufs rw,relatime,si=29428cce8ab9c340,dio,dirperm1 0 0
shm /var/lib/docker/containers/440054e41dc3f84d8aef2b6aadd28233155c69d324c57503d74f90b8a981eb05/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
shm /var/lib/docker/containers/b1fe8b73e04a021d69d3b1b79e33ed19be2df0c4ad93e77700691a3461e7485b/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/224a1f5dc06a nsfs rw 0 0
nsfs /run/docker/netns/920956113d66 nsfs rw 0 0
shm /var/lib/docker/containers/0ddc81f03a0d4429f0eae3206b2d20693a4a1f35a332be0ad79ab8ad5b98cf3e/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
shm /var/lib/docker/containers/644873504fdba9331840f835bc198d1ca567538aa6e0015abf1b1595a87a5471/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/1e374ae893e3 nsfs rw 0 0
nsfs /run/docker/netns/c0a777fcf70d nsfs rw 0 0
shm /var/lib/docker/containers/5439c7a24f07b96365e675853c2990062771152f963dd477f2d133c2450b132b/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
shm /var/lib/docker/containers/3194df531a73584cbd00c950f855463dd37ca1aade548d712cfdeff1a400714a/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
shm /var/lib/docker/containers/8959239b515cd94b1a81ed9b9712445e99682fa51132a62fbab8415f527ef550/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/995bf304995c nsfs rw 0 0
nsfs /run/docker/netns/4b4e8b4dd78f nsfs rw 0 0
nsfs /run/docker/netns/33ba6411ee56 nsfs rw 0 0
shm /var/lib/docker/containers/5b8080a252738d56e69f53e0886d6c5b75a149e557e60f7a4c0177a228642724/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/37adb01bb427 nsfs rw 0 0
shm /var/lib/docker/containers/5fdccfba075c9f5f287d7806c310f941a8f7d31ffad86250a1feed3f6c9f793e/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/e59811d19257 nsfs rw 0 0
shm /var/lib/docker/containers/514f0193c207597a36f52c063722a73663bd92e86b9e437c49a627c22d73c661/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/23cb6238c281 nsfs rw 0 0
shm /var/lib/docker/containers/4d9acb188667a753e3a87ddefe3b9c62ef7e79177550c06e9ad4a224c35e5461/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
shm /var/lib/docker/containers/f4ae70b144be0d4e68e49102c0c8be097c0a82907cfa6b3069ec35fad13c2817/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/abe97abd9d4c nsfs rw 0 0
nsfs /run/docker/netns/ff7a993f82d5 nsfs rw 0 0
none /var/lib/docker/aufs/mnt/c3f39565232f943995814de53b72b8ef53f11a5e186d8b0a3a86d7acb47b5b12 aufs rw,relatime,si=29428cc9adbed340,dio,dirperm1 0 0
shm /var/lib/docker/containers/0a2d80ff5667cb31a731617028e87e3ad7d96aa3e40b4852fa952b6dcb337852/mounts/shm tmpfs rw,nosuid,nodev,noexec,relatime,size=65536k 0 0
nsfs /run/docker/netns/bd1a7b4c204a nsfs rw 0 0
tmpfs /run/user/0 tmpfs rw,nosuid,nodev,relatime,size=3280624k,mode=700 0 0

@otherguy It seems that one does not have /dev/mapper entries. Mind sharing one which does? 😬

@victorgama I can but /dev/mapper entries are just LVM logical volumes. The feature should be universal and not only work on LVM mounts.
The columns in /proc/mounts are as follows (separated by 1 or more whitespace characters \s+ -- tabs and spaces both are allowed):

The 1st column specifies the device that is mounted.
The 2nd column reveals the mount point.
The 3rd column tells the file-system type.
The 4th column tells you if it is mounted read-only (ro) or read-write (rw) along with other special flags that are comma separated. E.g.: nosuid,nodev,noexec,relatime
The 5th and 6th columns are dummy values designed to match the format used in /etc/mtab

So right now you are displaying the device, gathered from sigar as I noticed. More helpful is the mountpoint though.
Not sure how sigar handles this but I assume it ignores "special" devices. If the first column is not a pointer on a filesystem, it's a "special" device, like all the Docker entries that you see in my example.
So in the list above, I removed all lines that do not begin with a slash (^[^/].*$) which leaves us with:
/dev/md2 / ext4 rw,relatime,data=ordered 0 0
/dev/md1 /boot ext3 rw,relatime,data=ordered 0 0

That means:

The device /dev/md2 is mounted on / and it's an ext4 volume that can be written (rw)
The device /dev/md1 is mounted on /boot and it's an ext3 volume that can be written (rw)

My preferred output would now be:
Mounts                         Size  Used  Free  Use%

/boot                          497M  218M  279M   44%
[===================================================]

/ (root)                       7.0G  3.0G  4.0G   43%
[===================================================]

Maybe make it configurable to show the device or mountpoint (like I mentioned initially, with mountpoints: yes), that should make everyone happy.

@otherguy Implemented and available to download. 🙌
No flag needed, just use your mountpoint as the disk name. It will first attempt to find a mountpoint, and falls back to the previous behaviour if none is found:
- type: disks
  disks:
#  - /dev/vda1
   - /

Again, thank you so much for the feedback!

@victorgama thanks! But this won't work if I don't specify any disks (instead displaying all of them), correct?

@otherguy That's unfortunately correct.
But it may still have a workaround: we can check whether both device and mountpoint begins with a forward slash when attempting to list all disks, but since we're relying on /proc/mounts to do that, I think that the "cleaner" version will only work on Linux for now.
I'll give it a try later today, and, if results are positive, I'll push another version right after. In the meantime, I'll leave this issue open.

Fixed in v0.2.2
Now '*' will list all known mountpoints instead of known devices.
(Which may cause devices to be listed twice, but I'm not sure what to do in this case)

Pretty awesome :)
Filesystems    Size  Used  Free  Use%
  /            7.0G  3.0G  4.0G   43%
  [=================================]
  /var         4.0G  1.1G  2.9G   28%
  [=================================]
  /home        2.0G   59M  1.9G    3%
  [=================================]
  /tmp         1.0G   34M  1.0G    4%
  [=================================]
  /boot        497M  219M  278M   45%
  [=================================]
  /perf        497M  303M  194M   62%
  [=================================]
  /tools         0     0     0     0%
  [=================================]


update image

The lsyncd latest version is 2.3.1, see below:
https://github.com/lsyncd/lsyncd/releases
The lsyncd version in docker image is 2.2.3, please help to update the docker image.

With https://github.com/RealOrangeOne/docker-lsyncd/commit/c7e3b5b419de8b43595bd086a1d0ca2cc576f591, the image should be rebuilt, and a newer version of lsyncd used.


please include /etc/nginx/*

In order to proxy php-fpm the file fastcgi_params is needed in /etc/nginx, thanks

This file was missing in the image.  It is now part of the latest image.


Not working

Error: Codeforces API is down.

Hey there, the new script for fetching test cases is in the works and should be ready in 3-4 days after testing. Thanks for hanging in there while we sort this out!
PEACE!


Next

@kruzikh please use https://github.com/ehn-digital-green-development/ehn-dgc-schema/compare/update_rat_sh
closing this PR. again.


Plugins

At the KubeCon BoF there were three hooks discussed to the core metadata DB (Grafeas core),

Producers  (for each artifact, metadata in different formats, from different toolss/sources)
Consumers (Analysis, prioritization, machine learning across metadata/artifact types)
Tooling to perform analysis across artifacts. Combine queried information to create risk scores. For example image reputation/signing, package importance/network accessible/utilization (e.g. openssl vs tar), history of packages risk (e.g. OpenSSL), CVSS score, runtime information etc.
Admission Control (based on authorization, policy etc)

Proposal for 2. Tooling across artifacts/risk assessment to be submitted soon

At least some of the tooling that we discussed may be blocked by https://github.com/Grafeas/Grafeas/issues/29. I'm working out how to best get open source list filtering into Grafeas, you should see progress there in the coming weeks.
@kudvanpk Are you planning to write tooling? I'm not sure if anyone else is actively working on tools at this point.

Some of the context was lost, so it's not clear whether there's a specific proposal or question that needs to be addressed here. Closing this due to the lack of activity, but please feel free to re-open with clarifications or open a new dedicated issue.


A basic implementation of tally rule

The tally rule works as follows:

For every digest we received from gossip, we assign a unique (incrementing) sequence number, and add the digest and validator name along with the sequence number to the a record table
At the end of each checkpoint, for each digest included in the checkpoint, we go over all validators that sent us this digest  in the order we received them (provided by the sequence number), and give them score based on the order.

It's very basic at the moment, and the score calculation is also very rough. We can tune and iterate on it.
TODO: Will add tests.

Update: We had an offline discussion, and there is still one open question. The follower-based tally rule does not check one's action against their reference gas price, which we will have to do on signatures rather than cert execution. Plan TBD

This is not the path forward.


Complete / integrate sqlite sqllogictest test scripts integrattion

Is your feature request related to a problem or challenge?
Part of https://github.com/apache/datafusion/issues/13811
@Omega359 has prototyped integration with the sqlite test suite ❤
This ticket tracks the remaining work to get this runner merged into datafusion main.
Describe the solution you'd like
I would like:

The runner merged into datafusion main
Clear instructions on how to run the suite

Bonus points would be some way to regularly run these tests
Describe alternatives you've considered
From https://github.com/apache/datafusion/issues/13470#issuecomment-2543328359

I've updated my test branch with the latest changes including adding skipif for Postgresql queries that fail to run. What is left is at least 19 legitimate query result mismatches where tickets were filed.
I've submitted a PR to the sqllogictest-rs repo for my changes but so far they haven't responded. If they do not get around to merging it for whatever reason we have two choices:

Rewrite the .slt files to be columnwise vs valuewise and change ordering to only be rowsort and remove the valuesort. I've actually written a lua script to handle the valuewise -> columnwise conversion, the second part will require some more work.
Fork the repo and use that.

For now I'm going to slow down work on this.

Additional context
No response

@Omega359  do I have this work described correctly?

Thanks for putting this together @alamb. Yes, the work is described correctly. CI builds currently are failing because of a clippy warning that I need to look into but otherwise it's good for others to look at.
I find that, at least on my machine, running the sqlite tests in 'normal' test mode takes ...forever. I typically run now with --release. Slower to build, faster overall.
cargo test --release --test sqllogictests -- --include-sqlite

One issue that I haven't fixed is that some of the sqlite test files are LARGE. In total the files are 763M. I am unsure that we would want them in the main repo ... and I am pretty sure they will fail a CI check with some being > 1MB anyways.
Perhaps we need a new datafusion_testing repository where these files would go and be linked into df via .gitmodules

Perhaps we need a new datafusion_testing repository where these files would go and be linked into df via .gitmodules

I think this is a good idea -- or maybe a script that checks out the original sqllite files or something
I also think we need to find a way to run it regularly (but likely it can't be on all PRs), see

https://github.com/apache/datafusion/issues/13845

@wiedld  from InfluxData expressed interest in helping move this project along. I will let her comment on what she next plans, etc

Yes, this seems like a perfect thing for a nightly ci run.
The thing that is holding me back atm is the sqllogictest-rs changes. Without those in the official repo means either redoing the output of the sqlite results (possible but not particularly easy) or using my fork. I'm hoping to get back to seeing if I can do the rewrite this weekend by comparing the sortmode results during a complete run (with my super hacked up version of sqllogictest-rs) and if they are the same write it out as columnmode. That would mean that the current runner would work.
I don't think attempting to pull in the original sqlite files will work as what I am producing is very different from what they have. datafusion_testing repo I think would be best.

Ok, I believe I'm ready to push a PR for the source code since the sqllogictest-rs folks pushed a release with my changes. I just need a decision on what to do with the actual sqlite .slt files. Do we:

Check them in as is and just adjust the large_files.yml in github workflow to let them through
git lfs
separate repo and use git modules for attaching to df repo (my preferred solution - datafusion-testing)
compress files in place and check in compressed files
something else?

separate repo and use git modules for attaching to df repo (my preferred solution - datafusion-testing)

yes this is my preferred solution too

What are the steps required to have a datafusion-testingcreated? I went hunting quickly through the apache docs I could find but I couldn't find the steps required

I did some poking around and found on this JIRA: https://issues.apache.org/jira/browse/INFRA-26314?jql=project %3D INFRA AND summary ~ "create repo" ORDER BY priority DESC%2C updated DESC

This can be done on a selfserve basis via https://gitbox.apache.org/boxer/. If you have any questions please feel free to email us at<EMAIL_ADDRESS>or find us on slack in #asfinfra.

I submitted a request

Your repository has been created and will be available for use within a few minutes.
Your project is available on gitbox at: https://gitbox.apache.org/repos/asf/datafusion-testing.git
Your project is available on GitHub at: https://github.com/apache/datafusion-testing.git
User permissions should be set up within the next five minutes. If not, please let us know at<EMAIL_ADDRESS>
It appears it is now available 🎉 : https://github.com/apache/datafusion-testing

Thank you very much @alamb. I'll work on the PR later today

Apparently there isn't a way to fork an empty repository in github, or at least I can't seem to find a way so I'm unable to push a PR there for the slt files. Can someone with contributor permissions push a license file to that new repo so that the github UI will allow me to fork it?

Apparently there isn't a way to fork an empty repository in github, or at least I can't seem to find a way so I'm unable to push a PR there for the slt files. Can someone with contributor permissions push a license file to that new repo so that the github UI will allow me to fork it?

Done. @Omega359

PR for data files: https://github.com/apache/datafusion-testing/pull/1


ETL9 information

Hi @Nippon2019
I loved your article, great work. Thanks for sharing.
I am training some neural networks with just Kanji characters and I'm block creating the modify_kanji method for ETL9. (as you did with ETL8). Do you happen to know where are the hiragana located inside ETL9 to delete them? Similar to what you did in /Kanji/modify_kanj.py#L18
I couldn't find the information in the original source.
I really appreciate your help

Hi @pyjavo
Thanks for reading my article!
Yeah that was actually one of the reasons I decided not to train on ETL9 in the end, because I didn't know the exact content of it and I didn't want to spend time figuring it out. Looking back at the original source though, it says that あ has data 'A.HI', so I'm guessing that the Hiraganas in ETL9 would have data ending in '.HI'. Something similar to what I did in /Hiragana/read_hira.py#L21 and changing the if b'.HIRA' to if not b'.HI' might work.
I hope that helps! lmk if you have any other questions, I'd be happy to help!


The help of numpy.random.choice is not complete

I found the help information of numpy.random.choice is not complete. It only have the function declaration.

I presume that you're looking for a docstring or other documentation?
The type information and docstrings come from numpy itself. If you right-click on choice and select "Go To Declaration", you'll see which file this information comes from. In the latest release of numpy, choice is declared in a type stub file numpy/random/mtrand.pyi. Unfortunately, it doesn't include any docstrings, so pylance has nothing to display. You may want to file a bug (or better yet, a PR) in the numpy github repo.

Thank you, I have asked for numpy

Putting type information only in pyi files is standard.  docstrings are not incorporated in these files generally.  Other IDEs, e.g., PyCharm, can seamlessly incorporate pyi information with standard docstrings. I don't expect NumPy, or many other projects that have compiled code and use pti for typing, will move their docstrings away from the code into type stub files.
Related to numpy/numpy#20809

https://github.com/numpy/numpy/issues/20809#issuecomment-1012013047
According to this, it seems to be pylance's or python-extention's problem.

numpy/numpy#20809 (comment)
According to this, it seems to be pylance's or python-extention's problem.

Following up on this comment: the issue seems to be limited to functions that are purely C- or Cython-based, lacking any wrapper of some sort written in pure-python.

@BvB93 Do the examples of functions with python wrappers have docstrings and typing information together. or is the docstring in the .py file and the typing in a .pyi?

I don't know what is python wrappers. But in numpy  1.20.3 version, I right-click on choice and select "Go To Declaration". I can't found any docstrings or typing information.

@BvB93 Do the examples of functions with python wrappers have docstrings and typing information together. or is the docstring in the .py file and the typing in a .pyi?

The docstrings and annotations are always split between .py/.pyx and .pyi files.
Just to give a few more examples from my previous point:
Shows docstrings

np.atleast_2d: Pure python function
np.bincount: C-based function with some form of python wrapper

Does not show docstrings

np.random.choice: Cython function
np.array: C-based function without a python wrapper

I see. bincount's python wrapper is
https://github.com/numpy/numpy/blob/8dbd507fb6c854b362c26a0dd056cd04c9c10f25/numpy/core/multiarray.py#L884
while it's type information is here
https://github.com/numpy/numpy/blob/e2d35064df262efa6eb7dfe5bfc43160c73cf685/numpy/core/multiarray.pyi#L417

Pylance will find and display docstrings for functions and classed declared in ".pyi" files if it can find the same symbol in a corresponding ".py" file. In the case of np.random.choice, there is no corresponding ".py" file though. When functions are implemented in a language other than Python, there is no static way to access the docstring if it's not in the ".pyi" file. As such, it is recommended that the ".pyi" include the docstring. Refer to this guidance for more details.

This issue has been fixed in version 2022.1.3, which we've just released. You can find the changelog here:  CHANGELOG.md


Let everyone know that we don't support html tags

Close #47
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Fix no-ec (again)

We broke no-ec again. I only just fixed it this morning :-)
This PR is mainly about fixing no-sm2, and then if no-ec is requested then this implies no-sm2.

Checklist

[ ] documentation is added or updated
[ ] tests are added or updated

I was about to make a similar fix

I have some additional fixes related to SM2 and no-sm3.

Pushed. Thanks.

I have some additional fixes related to SM2 and no-sm3.

Great. Anything urgent, or can it wait until after the beta?

I think this should be closed?

Oh, right! Yes - thanks. This was merged.