小文件较多场景下，raft心跳超时，leader切换异常

CFS Version: 2.4 Release
SYSTEM: Centos 7.3
NODE: 18台（metanode\datanode混合部署）
服务配置：128G RAM、HDD: 6T*12  no raid
从2.3版本升级到2.4时，更新metanode后出现以下现象，具体日志同步给@Shuoran Liu
在2.2版本之前由于小文件多，dp较多，修改过以下参数：
metanode/raft_server.go：
    raftConf := &raftstore.Config{
            NodeID:            m.nodeId,
            RaftPath:          m.raftDir,
            IPAddr:            m.localAddr,
            HeartbeatPort:     heartbeatPort,
            ReplicaPort:       replicaPort,
            TickInterval:      2000,
            NumOfLogsToRetain: raftstore.DefaultNumOfLogsToRetain * 2,
    }

升级到2.3同步修改，目前升2.4依然同步修改。2.2--> 2.3时同样出现该问题，2.3 --> 2.4问题依旧，望重现解决，谢谢！
metaNode_error.log:
2021/06/10 17:58:29.415005 [ERROR] manager_proxy.go:77: [serveProxy]: req: 9649638 - OpMetaInodeGet, no leader
2021/06/10 17:58:29.516050 [ERROR] manager_proxy.go:77: [serveProxy]: req: 9649638 - OpMetaInodeGet, no leader
2021/06/10 17:58:29.617135 [ERROR] manager_proxy.go:77: [serveProxy]: req: 9649638 - OpMetaInodeGet, no leader
2021/06/10 17:58:29.718326 [ERROR] manager_proxy.go:77: [serveProxy]: req: 9649638 - OpMetaInodeGet, no leader
Raft log:
2021-06-10 17:58:23,507 raft_fsm_candidate.go:37: [DEBUG] raft[80] became candidate at term 164.
2021-06-10 17:58:23,507 raft_fsm_candidate.go:134: [DEBUG] raft[80] received vote from 16 at term 164.
2021-06-10 17:58:23,507 raft_fsm_candidate.go:117: [DEBUG] [raft->campaign][80 logterm: 161, index: 485780] sent vote request to 24 at term 164.   raftFSM[0xc00a788000]
2021-06-10 17:58:23,507 raft_fsm_candidate.go:117: [DEBUG] [raft->campaign][80 logterm: 161, index: 485780] sent vote request to 85 at term 164.   raftFSM[0xc00a788000]
2021-06-10 17:58:23,508 raft_fsm_candidate.go:136: [DEBUG] raft[80] received vote rejection from 24 at term 164.
2021-06-10 17:58:23,508 raft_fsm_candidate.go:84: [DEBUG] raft[80] [q:2] has received 1 votes and 1 vote rejections.
2021-06-10 17:58:23,508 raft_fsm_candidate.go:136: [DEBUG] raft[80] received vote rejection from 85 at term 164.
2021-06-10 17:58:23,508 raft_fsm_candidate.go:84: [DEBUG] raft[80] [q:2] has received 1 votes and 2 vote rejections.
2021-06-10 17:58:23,508 raft_fsm.go:385: [DEBUG] raft[80] random election timeout randElectionTick=5, config.ElectionTick=3, randTick=2
2021-06-10 17:58:23,508 raft_fsm_follower.go:32: [DEBUG] [raft][80] became follower at term[164] leader[0].
2021-06-10 17:58:31,526 raft_fsm.go:208: [DEBUG] [raft->Step][80 term: 164] received a [ReqMsgVote] message with higher term from [85 term: 165].
2021-06-10 17:58:31,527 raft_fsm.go:385: [DEBUG] raft[80] random election timeout randElectionTick=5, config.ElectionTick=3, randTick=2
2021-06-10 17:58:31,527 raft_fsm_follower.go:32: [DEBUG] [raft][80] became follower at term[165] leader[0].
2021-06-10 17:58:31,527 raft_fsm_follower.go:98: [DEBUG] raft[80] [logterm: 161, index: 485780, vote: 0] voted for 85 [logterm: 161, index: 485789] at term 165.
2021-06-10 17:58:31,527 raft.go:575: [WARN.] raft:[80] elected leader 85 at term 165.
2021-06-10 17:58:31,527 raft_fsm_follower.go:174: [DEBUG] raft[80 logterm: 0, index: 485789] rejected msgApp [logterm: 161, index: 485789] from 85

@shuoranliu 日志文件有吗？同步给我一下


Upgrade to Vaadin 24

Tried running it locally, none of the filters show up

Maybe this works now...


High memory usage on invalid instrumentationkey

On Microsoft.ApplicationInsights.AspNetCore v2.1.1

dotnet new api
In Visual Studio: Right-click project -> Add -> Add Application Insights

Calling the api produces the following output:
Application Insights Telemetry (unconfigured): { ... }
Memory usage is fine. Doesn't grow hard when calling the api multiple times.

In Program.cs, change UseApplicationInsights() to `UseApplicationInsights("invalid_guid").

Calling the api produces the following output:
Application Insights Telemetry: { ... }
Memory usage grows pretty hard when calling the api multiple times. In the memory snapshot there are a lot of extra objects with references to ApplicationInsights.
Expected:
When the guid is invalid (or the appinsights endpoint cannot be reached with a valid guid), start ApplicationInsights in Unconfigured mode. Or at least don't buffer all the telemetry.
See: https://github.com/nphmuller/AppInsightsMemory for an easy repro.

@nphmuller, thank you for reporting the issue and providing the full repro!


Inequality symbols in available symbols causes issues

If you type x, y, <=, sin() etc in the available symbols list for a symbolic question, then the behavior is as expected for everything except the <= sign.
This gets parsed as a symbol, displays as a symbol and then gets treated like a symbol (NOT like an operator as it should):

give python: 3 * <= * y which is clearly wrong, but the user would never know because the result shows up like:

I think this was fixed in https://github.com/ucam-cl-dtg/isaac-app/commit/67c2254f83c79e866e1cf62f7ce053890fcf63bf, and it's certainly fixed now.


Improving storage of graph metadata

Currently the format for storing metadata of the graph (database, infiles, edges, ...) in the graph creation module is a little confusing. Maybe looking into storing metadata of the sources, edges, etc. in a more centralized format (f.e. json) could improve readability. Further as sources can change at anytime (seperator, urls, ...) this would help in adatpting to these changes faster and would make  including new sources/edges easier.

Do you think we could standardize everything to RDF?

Yes that might be even better than JSON. With RDF we could provide more readability than the current method (storing metadata in seperate static python classes), while still having the modularity of the current method.

I guess than we should try to transition to RDF!
One potential problem is of course that sometimes the triples make it a bit cumbersome to capture N-ary relationship with N>3. But that is probably not a problem for the dataset descriptions.


_divergence! without [l,m] access to LTM

@maximilian-gelbrecht I realised we didn't propagate the @inbounds for setindex!(::LowerTriangularMatrix,...) -- the last commit does that. However, I'm not sure how to best test that because it can create a segfault to write outside the data range. I've done it once on my laptop and killed the session, so I believe that's a good sign 🤣 Uncommented these tests as they obviously shouldn't run regularly with CI...


PSA-2023-31901 - Several files in error, unable to determine why

Describe the bug in current situation
Several files on PSA-2023-31901 are in error (multiple .msg, one .doc). Other files in error are the result of being password protected. Unable to determine why other files are in error, and more investigation needed.
Link bug to the User Story
Impact of this bug
Describe the impact, i.e. what the impact is, and number of users impacted.
Chance of Occurring (high/medium/low/very low)
Pre Conditions: which Env, any pre-requesites or assumptions to execute steps?
Steps to Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

Actual/ observed behaviour/ results
Expected behaviour
A clear and concise description of what you expected to happen. Use the gherking language.
Screenshots/ Visual Reference/ Source
If applicable, add screenshots to help explain your problem. You an use screengrab.

Will investigate outside ticket, and if bugs found, create new bug ticket.


Update memberships.yml

Updated the broken links for logos. Please review.

 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.

@paras-jain Are the link broken? They look fine to me. 🤔
https://twitter.github.io/memberships
The current links are the URL to their Twitter profile image, which is intended, since Twitter ;-)

Oh, site preview on firefox did not show the logos.

Checked on edge, it's fine.


Raft package fixes

This commit includes various fixes to improve the stability of the raft package tests and benchmarks.

initial review complete, would like to get feedback on the questions, and can then take another pass.

+1, and we can re-commence testing.


Adjusting min-lr in cosine schedule to batch and world size

The peak learning rate is scaled according to lr = base_lr * batch_size * world_size / 512, but this adjustment does not appear to be made for the min learning rate of the cosine schedule, which seems to be fixed at 1e-5.
This implies that using a smaller batch size will shrink the range over which the learning rate decays. Is this intended behaviour?

Hi @nasimrahaman,
Yes you are absolutely right but the scaling of min lr should not follow the same rule as the peak Learning rate. We did not study how to scale it well so we left it like that by default.
Best,
Hugo


issue #4733 Update SourceWorker.java

lin line 279 e.printStackTrace() function has be removed removed
<

@Pil0tXia  i have  made change in a class
SourceWorker class.
i have  gone through with  other two classes also but their is  no change.
please review my  work

@archit-8
Please supplement modifications to the usage of e.printStackTrace() in the following two classes:

org.apache.eventmesh.runtime.client.impl.PubClientImpl
org.apache.eventmesh.common.ThreadWrapperTest

Additionally, please submit a PR in the standard format, including PR title and the "Fixes" keyword in the PR body.


[coepi-backend-aws]: Create a domain api.coepi.org and redirect the Cloud API endpoint to that URL

Is there any reason why we shouldn't do this via Route53?

I don't see why not. Just confirm with Scott

Not sure where we left this after the Slack conversation. It's easier for me to do the CNAME / A record directly with my registrar than to delegate a zone to R53 if we're just doing the single hostname. But if there are significant advantages to delegating api.coepi.org to R53, also happy to do that. If not, just LMK what hostname. you want it CNAMEd to.

The current working endpoint that can be CNAMEd to is this one ->  https://18ye1iivg6.execute-api.us-west-1.amazonaws.com
The full API endpoint for v4 looks like this:
https://18ye1iivg6.execute-api.us-west-1.amazonaws.com/tcnreport/v4
which should translate to
https://api.coepi.org/tcnreport/v4
We can then use the below strategy to keep the same hostname and proceed with versioning:
https://dzone.com/articles/api-versioning-approach-with-aws-api-gateway

@scottleibrand @bhushanRamnani The issue is that endpoints exposed by API Gateway are not "fixed" if the API gateway is recreated - this means that we'd have to get @scottleibrand to update the CNAME manually every time the API Gateway is (re)created if we just point the existing CNAME to the AWS API Gateway.
Best option is to set up a "custom" fixed API DNS in R53 that doesn't change and have @scottleibrand point his CNAME at that, I think?

Ok, I'll CNAME api.coepi.org to 18ye1iivg6.execute-api.us-west-1.amazonaws.com for now, and can update that to point to a R53 target once y'all create it.

Getting a certificate error ->
f0189818d391:~ ramnanib$ curl -X GET https://api.coepi.org/v4/tcnreport
curl: (35) error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol


Fix typo on documentation link

The old link information was showing authentication-oauth1 when it should be authentication-jwt

Thank you


Updated services

@peb-adr Note: UPDATE positions SET information=NULL  in postgres required in new version


[Dev][Tips] Dynamically fetch list of tips

Currently, the tips page is using a hardcoded file to create the tips page.
It should be fetching all the docs files.
It seems that fetching data from a markdown file to display part of its content an enable a filter is not trivial.
Acceptance Criteria

[ ] Fetch data from docs markdown metadata and display it in the Tips Page as a card
Display title and description only
Add level and tags later in other issues

So with the research I've done so far, we may be able to do it using MDXProvider component. I will try it out today and see if it works.

Hey all, I added the getFrontmatter.js script and it needs review. I tested it locally and it works but I didn't want to commit the completed file because it would involve rebuilding the site—which would involve 589 or so changes 😨
This takes care of fetching the frontmatter dynamically and outputting it to a file to use in the website before it's built.
TODO

We need to refactor tips.js, or change the output directory in getFrontmatter.js so the two can work in tandem
We need to do some UAT before we can close this issue out to ensure everything displays correctly.

Follow up for this issue will be Issue #464

@aquaomarine do you have a solution? can this issue be closed?

Solved my adding https://mdxjs.com/ as a script folder
Closed in the #459 PR


Dispose of comments (Inform stage)

link to issue #930

Dispose of comments
update strategy content

1st round of review completed
2nd round of review started


fix the version of azure-functions-java-library in function's integration test

Codecov Report

Merging #220 into develop will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff            @@
##           develop     #220   +/-   ##
========================================
  Coverage    58.61%   58.61%
========================================
  Files           50       50
  Lines         1590     1590
  Branches       176      176
========================================
  Hits           932      932
  Misses         596      596
  Partials        62       62

Continue to review full report at Codecov.

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Release/1.12.1

version 1.12.1

:+1:

Current coverage is 68.29% (diff: 100%)

Merging #105 into master will not change coverage

@@             master       #105   diff @@
==========================================
  Files            18         18
  Lines           880        880
  Methods           0          0
  Messages          0          0
  Branches         44         44
==========================================
  Hits            601        601
  Misses          235        235
  Partials         44         44

Powered by Codecov. Last update 5d219f2...85f8cb4

👍


Enable back Windows native-image job

(Will probably only run the Windows native ITs from master, and not on PRs…)


Fixed running tests as a user.

Added missed sudo in playbooks.
Added logging directory creation for compatibility test suite.
Added setting owner for logging directory.
(There are two logging directories in tests: directory for dnet_ioserv
process and directory for client. The first one is used by a root process and
the second one is used by client process which is running as test-user (from
--user option of running/runtests.py))
Added missed sudo for test_helper.network module's functions.
Get rid of depricated networking functions.
(Replaced drop_node, resume_node, resume_all_nodes methods of
EllipticsTestHelper from test_helper.elliptics_testhelper with proper
functions of test_helper.network module and removed those methods. Moved
set_networking_limitations and clear_networking_limitations from
test_helper.elliptics_testhelper to test_helper.network)

reviewers: @uvizhe

ok


508: Error Suppression Clone Pop-out Focus

When closing the Clone module, focus does not return to the Clone button

Closed ticket based on discussion with CAMD on 3/4/24. Before deployment there will be a scan performed and any issues will be remediated at that time.


BUG @Size is ignored in properties using collections when using oas 3.1.0

Problem
When generating OpenAPI 3.1.0 spec the @Size annotation on property with a collection type is ignored. The expected behaviour is that the generated property has both maxItems and minItems set but these properties are not found in the generated open api.
Expected behaviour
@Size#min is used to generate minItems and @Size#max is used to generate maxItems for the generated property schema
Reproducer
The issues is reproduced in the following test:
    @Test(description = "Shows that @Size is not correctly handled in properties using collections when using oas 3.1.0")
    public void testModelUsingCollectionTypePropertyDoesNotHandleSizeAnnotationForOas31() {

        String expectedYaml = "DtoUsingSizeOnCollection:\n" +
                "  type: object\n" +
                "  properties:\n" +
                "    myField:\n" +
                "      maxItems: 100\n" +
                "      minItems: 1\n" +
                "      type: array\n" +
                "      items:\n" +
                "        type: string";

        Map<String, io.swagger.v3.oas.models.media.Schema> stringSchemaMap = ModelConverters.getInstance(true).readAll(DtoUsingSizeOnCollection.class);
        // fails as the maxItems/minItems will not be added to the schema of myField for oas 3.1.0
        SerializationMatchers.assertEqualsToYaml31(stringSchemaMap, expectedYaml);
    }

    public class DtoUsingSizeOnCollection {
        @Size(min = 1, max = 100)
        private List<String> myField;

        public List<String> getMyField() {
            return myField;
        }

        public void setMyField(List<String> myField) {
            this.myField = myField;
        }
    }

Investigation with proposed solution
Looking at the ModelResolver.applyBeanValidatorAnnotations code (which is where information from bean validation annotations are processed), there is a check that the property input parameter of type Schema is an instance of ArraySchema. If the check succeeds then the information from @Size is propagated to the generated schema (using the minItems/maxItems properties). Nevertheless for open api 3.1.0 property will be of type JsonSchema instead of ArraySchema and therefore the information from @Size will not be used. A possible solution would be that instead of using (property instanceof ArraySchema) a check is performed on the type/types fields of property to ensure that the property is an array schema.

@Lorenzo-Bracci thank you for reporting this issue. Fixed by: https://github.com/swagger-api/swagger-core/pull/4734 and will be part of next release


Add header examples

Changes proposed in this Pull Request:

Drawer Header Examples Page

Can you do the line-highlighting for the line where the header appears
Are <blui-drawer-header>s supposed to be in <blui-drawer-body>s?
Is it possible to add more room here:

Like this:

Now that you have the examples, please take this out of the API Docs page

Thanks @huayunh , PR has been updated.

There are two more bullets in my first comment that you may want to attend to

There are two more bullets in my first comment that you may want to attend to

Oops, I missed those ones.  Good catch on the drawer-header being in the drawer-body.  That's fixed.
I've also added line-highlighting but not in love with how it looks right now.

want to take out those line numbers too? They've always felt strange to me.

want to take out those line numbers too? They've always felt strange to me. I personally like the line highlighting, as it guides attention better

You got it, this is already looking a lot better.

you have my design thumbs up!
I didn't check the code... I don't Angular.

Changes looks fine 👍 .
Can we add space between example and code block?


Local rebuilds fail, but clean builds work

Reproduce:

run pip install -e . with a local copy (works)
run it again (crashes with unhelpful output)

Workaround: rm ./build/ between runs, but you lose your build cache which makes development tedious

Better workaround, but still not ideal:
rm build/temp.*/CMakeCache.txt; pip install -e .

The difference between CMakeCache.txt on fresh builds, and rebuilds is:
ben@ben-precision-3630:~/repos/gtsam_quadrics$ diff build_success/temp.linux-x86_64-3.8/CMakeCache.txt build_fail/temp.linux-x86_64-3.8/CMakeCache.txt
26,27c26,27
< //Build shared gtsam library, instead of static
< BUILD_SHARED_LIBS:BOOL=OFF
---
> //No help, variable specified on the command line.
> BUILD_SHARED_LIBS:UNINITIALIZED=OFF
197c197
< CMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-w8v9k1rc/overlay/bin/ninja
---
> CMAKE_MAKE_PROGRAM:FILEPATH=/tmp/pip-build-env-zabdl3u3/overlay/bin/ninja
882c882
< CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=40
---
> CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
967,968d966
< //ADVANCED property for variable: GTSAM_COMPILE_DEFINITIONS_PUBLIC
< GTSAM_COMPILE_DEFINITIONS_PUBLIC-ADVANCED:INTERNAL=1

Issue is due to the caching of CMAKE_MAKE_PROGRAM (using a /tmp/pip-build-env directory which is unique on every build).
Need to figure out how to stop this caching.


Add app to automatically update dependency versions

The update-dependencies .NET app must be invoked from the root of the
repo.  A update-dependencies.ps1 script is also provided which installs
the .NET CLI and then compiles and invokes the app; this script can be
invoked from anywhere.
The plan is for Maestro to invoke a VSTS build definition whenever a new
CLI build is available, which will invoke the update-dependencies.ps1
script.
Also add a .gitignore file.
cc: @MichaelSimons

Here is a sample PR created with this app, using my fork of the repo:
https://github.com/naamunds/dotnet-docker-nightly/pull/1

One minor comment, other than that it looks good.


Fix waitTime when TimeUnit is not MILLISECONDS and leaseTime is not set

When we do a tryAcquire without leaseTime, TimeUnit is forced to MILLISECONDS even if waitTime is not in MILLISECONDS. This can cause inconsistency and lead to troubles.

Thank you for purposed changes. This value is converted in the method implementation.

Imagine you do :
this.lock.tryLock(30, SECONDS)
In tryAcquireAsync I enter in this code :
ttlRemainingFuture = tryLockInnerAsync(waitTime, internalLockLeaseTime,
TimeUnit.MILLISECONDS, threadId, RedisCommands.EVAL_LONG);
With waitTime 30 (seconds) and internalLockLeaseTime 30000 (milliseconds)
Finally in tryLockInnerAsync :
if (waitTime > 0) {
wait = unit.toMillis(waitTime);
}
With waitTime 30 and unit MILLISECONDS, so wait is 30


SparkDataFrameLocator: Allow locator with no index

Even if no index is provided, if there is no slice selection
provided in the Locator - it should work. As the index
is not required and can be anything.
Fixes https://github.com/databricks/spark-pandas/issues/55

Was looking through this again, and realized even for the multiindex case - we already support column indexing. And row indexing when slice is : is a no-op scenario.
So, added a check on the top to not worry about the indexing schema and so on when slice is :
This enables doing .loc[:, ['a', 'b']] in multi index dataframes too - which was erroring out earlier


Svg inject

One issue remaining is that transitive dependencies don't resolve, so injection requires adding jquery, svg-injector, and vizlab-js to the page resources.  There is an example using this in example.

Coverage increased (+0.02%) to 77.403% when pulling 63ccd68fa26bbbe451974d98d7d4d119b3ce825a on jiwalker-usgs:svg-inject into ec82b6fe0a3de525d688f8ec29df751847e35589 on USGS-VIZLAB:0.2.x.

"There is an example using this in example." You mean the example viz? Could you push that up (or did I miss it...)?

It actually added to the previously open PR https://github.com/USGS-VIZLAB/example/pull/12


[release-1.21] fix TestReadSignedCertificate

This is an automated cherry-pick of #51051

@istio-testing: The following test failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name
Commit
Details
Required
Rerun command

analyze-tests_istio_release-1.21
450b2507b52b292f0702a79ae06847b86da874d6
link
true
/test analyze-tests

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository. I understand the commands that are listed here.

/retest-required

@istio-testing: The following test failed, say /retest to rerun all failed tests or /retest-required to rerun all mandatory failed tests:

Test name
Commit
Details
Required
Rerun command

integ-pilot-multicluster_istio_release-1.21
450b2507b52b292f0702a79ae06847b86da874d6
link
true
/test integ-pilot-multicluster

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository. I understand the commands that are listed here.

/retest-required


question about copy artifacts filter spec fix #1830

About this failed build https://ci.adoptopenjdk.net/job/build-scripts/job/jobs/job/jdk11u/job/jdk11u-windows-x64-openj9-windowsXL/364/
06:44:54  Copied 0 artifacts from "build-scripts » release » create_installer_windows" build number 4410
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // node
[Pipeline] echo
06:44:54  Execution error: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/OpenJDK*jdk_*_windows_*.msi

https://ci.adoptopenjdk.net/job/build-scripts/job/release/job/create_installer_windows/4410/console
had produce : OpenJDK11U-jdk_x64_windows_openj9_windowsXL_2020-06-05-23-31.msi
At the begining I was thinking the filter was bad because I have only see _windowsXL doesn't match _windows_ .. but there is a _windows_ before _windowsXL .. so the filter must have been matched.
Why OpenJDK*jdk_*_windows_*.msi havn't matched OpenJDK11U-jdk_x64_windows_openj9_windowsXL_2020-06-05-23-31.msi
seeing copyArtifacts filter doc : https://www.jenkins.io/doc/pipeline/steps/copyartifact/

See the @includes of Ant fileset for the exact format.

I have juste tested with ant :
<project name="TestProject" default="testfilter" basedir=".">
    <target name="testfilter">
        <copy todir="/tmp/dst" overwrite="true" verbose="true">
                <fileset dir="/tmp/src" includes="wix/ReleaseDir/OpenJDK*jdk_*_windows_*.msi" />
        </copy>
    </target>
</project>

ant

testfilter:
     [copy] Copying 1 file to /tmp/dst
     [copy] Copying /tmp/src/wix/ReleaseDir/OpenJDK11U-jdk_x64_windows_openj9_windowsXL_2020-06-05-23-31.msi to /tmp/dst/wix/ReleaseDir/OpenJDK11U-jdk_x64_windows_openj9_windowsXL_2020-06-05-23-31.msi

BUILD SUCCESSFUL
Total time: 0 seconds

Either copyartifact don't exactly use exact filter format as Ant fileset @includes
either the filter was not the problem.

I thinking it must have matched like this when there was the first error : OpenJDK(11U-)jdk_(x64)_windows_(openj9_windowsXL_2020-06-05-23-31).msi

For the record, the failed match was on build-azure-win2012r2-x64-2. Later builds seem to be doing better, one on the same machine which passed.
@karianna was changing up how we copy artefacts from build to build yesterday. It's possible this may have fixed it. I'll keep an eye on it over the next week to see if this reoccurs

Later builds look ok. I'm going to put this under "fixed by copy artifact" changes. This can always be reopened if we see it again

This is strange. It seems to be an intermittent problem I'm seeing in the build scripts.
I've seen two instances of this in the nightlies last night

https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk14u/job/jdk14u-windows-x64-openj9/105/console (Installer ran green) failed with this

04:37:24  Execution error: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/OpenJDK*jdk_*_windows*.msi

But a build two days before that, passed https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk14u/job/jdk14u-windows-x64-openj9/103/console

https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk11u/job/jdk11u-windows-x64-openj9-windowsXL/371/console (Installer ran green again) failed with the same error as above. Again, the build two days before passed https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk11u/job/jdk11u-windows-x64-openj9-windowsXL/369/

Keeping in mind my changes to windows installer went in over a week ago (except for https://github.com/AdoptOpenJDK/openjdk-build/pull/1830), I don't think it's due to that.
I'm seeing
Done Adding Additional Store
Successfully signed: ReleaseDir\OpenJDK11-jdk_x64_windows_openj9-<IP_ADDRESS>.msi

Done Adding Additional Store
Successfully signed: ReleaseDir\OpenJDK11-jdk_x64_windows_openj9-<IP_ADDRESS>.msi

in https://ci.adoptopenjdk.net/job/build-scripts/job/release/job/create_installer_windows/4565/console and
Done Adding Additional Store
Successfully signed: ReleaseDir\OpenJDK14-jdk_x64_windows_openj9-<IP_ADDRESS>.msi

Done Adding Additional Store
Successfully signed: ReleaseDir\OpenJDK14-jdk_x64_windows_openj9-<IP_ADDRESS>.msi

in https://ci.adoptopenjdk.net/job/build-scripts/job/release/job/create_installer_windows/4563/console (the same installer jobs ran for the builds I linked above).
So to resolve this, I'm guessing I would need to update the filter to be ReleaseDir/OpenJDK*jdk_*_windows*.msi but that doesn't explain why other jobs, like this one manage to copy the artifacts over fine.
@douph1 Any ideas?

I'm testing the theory I mentioned above with a temp PR https://github.com/AdoptOpenJDK/openjdk-build/pull/1856

Also see #1858

I'm testing the theory I mentioned above with a temp PR #1856

Test theory wasn't successful

https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk14u/job/jdk14u-windows-x86-32-hotspot/109/console
22:35:58  Copied 0 artifacts from "build-scripts » release » create_installer_windows" build number 4769
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // node
[Pipeline] echo
22:35:58  Execution error: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/*

Is that because of permissions or something else though...

I have see lot of this error "Failed to copy artifacts" on internet with a stacktrace  .. I don't know how but did you think we can print stacktrace together with the error message ?

@douph1 It doesn't look like it is printing the full trace still 😭
https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk14u/job/jdk14u-windows-x64-openj9/116/console
08:18:25  Scheduling project: build-scripts » release » create_installer_windows
08:18:33  Starting building: build-scripts » release » create_installer_windows #4896
[Pipeline] copyArtifacts
08:24:18  Copied 0 artifacts from "build-scripts » release » create_installer_windows" build number 4896
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // node
[Pipeline] echo
08:24:18  Execution error: hudson.AbortException: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/*

I'm not a groovy export, I have just seen this syntax in the script using ${e} and I don't have made my homeworks :(
Maybe context.println "Execution error: " + e.printStackTrace()
is better ?

It's worth a shot 🤷

wait
see https://issues.apache.org/jira/browse/GROOVY-3947
https://issues.jenkins-ci.org/browse/JENKINS-44808
first

it will be harder after next jenkins update to see stactrace for non-administrator :

https://www.jenkins.io/changelog-stable/
Suppress error stack traces for non-administrator users as core capability. (issue 60410)
https://issues.jenkins-ci.org/browse/JENKINS-60410

https://ci.adoptopenjdk.net/view/Failing Builds/job/build-scripts/job/jobs/job/jdk11u/job/jdk11u-windows-x64-openj9/649/console
05:13:33  Copied 0 artifacts from "build-scripts » release » create_installer_windows" build number 5075
[Pipeline] }
[Pipeline] // stage
[Pipeline] }
[Pipeline] // node
[Pipeline] echo
05:13:33  Execution error: hudson.AbortException: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/*
[Pipeline] }
[Pipeline] // timeout
[Pipeline] }
[Pipeline] // timestamps
[Pipeline] End of Pipeline
ERROR: Failed to copy artifacts from build-scripts/release/create_installer_windows with filter: wix/ReleaseDir/*

Still no stacktrace unfortunately. Could we perhaps roll it back and just do printstacktrace and get admin permission to do so?

Renamed to make it more appropriate as this no longer a question

I suspect @andrew-m-leonard fixed this when he increased the job retention as I haven't seen this for a while now


Reactome release 82 models with correct contributor

A repeat of #245 but with the code fix included to correctly emit GOC:reactome_curators as contributor.
This load is from https://github.com/geneontology/reactome-go-cams/pull/9.

dev always good.


Loss socialisation story telling

If your PnL is lower than you were expecting it may be because you experienced loss socialisation.
As a user of the console I want the UI to tell me this has happened (and why?)
MVP - transfers view by market/transfer type in a table.
price change: mark to market transfer..... do one row that aggregates (expand button). Discuss with Barney if needed.
Scope of this is to get an MVP out to the users and expand post trading being enabled.

Initial thoughts here:
https://www.figma.com/file/K49Nx7XfocShhHcwwQzQkm/Console-V2?node-id=2276%3A30549
A toast would be shown when loss socialisation occurs:

And then shown under the history tab:

Worth someone sense checking the statement in the ticket description

If your PnL is lower than you were expecting it may be because you experienced loss socialisation.
Does your PnL appear lower or do you just have your position reduced in size and "realise" a profit/loss early?

IMO the key place all storytelling about your balance/P&L happens is the ledger entries view. I am not really sure what story telling would be needed for loss socialisation beyond making sure it's shown properly in the ledger view and maybe highlighting that it had happened to a position (annotation on position view linking to the filtered ledger entries for loss socialisation on that market?), or showing a notification, or something like that.
It's important to remember that if Vega works well then loss socialisation will almost never happen in mainnet. It might happen a bit more early on if things go wrong in odd ways, but in general it ought to be rare. It's also ubiquitous among derivatives platforms in crypto particularly and I've never seen any giving it much attention. The financial adjustment would just show up as aa line item in your accounting / balance history (i.e. ledger entries) view on any other plaform.
I'm not sure we have enough evidence it'll happen often or that much more than the ledger entries view is needed to build anything bespoke for this without real mainnet feedback, given the number of other improvements we could make.
But very happen to put this out to wider discussion and prioritisation, it'd just  be good to have that discussion before we spend a lot of time on something like this.

@campbellssource re: your question:

Does your PnL appear lower or do you just have your position reduced in size and "realise" a profit/loss early?

Your total (general + margin for the market) balance of the settlement asset, and therefore P&L, would be lower than you would have calculated and would expect purely based on your entry price and the current market price and/or the price you closed the position at if loss socialisation had been applied, yes.


Feature/octopus pack

Created a new pack for Octopus Deploy, Octopus Deploy is one of the most popular DevOps tools for the .NET stack.
The pack includes the key tasks

create a release of a project
deploy a release of a project
get a list of releases for a project

The config file takes the api_key hostname and port of the Octopus API server.

<3 it. Just the two comments.

What others have said - nice work :+1:


Add methods for getting primitives with absolute position

Coverage increased (+0.09%) to 95.391% when pulling 87826b61644ecf351f3079e44367c37055e9d404 on niketh:master into 8b1547d58a7b62d604066fca0dbad08731f8d049 on DataSketches:master.


Metadata not recognized when file starts with BOM

When a content file starts with a UTF8 BOM I don't get any metadata which can result in hard-to-find bugs. We're using Wintersmith to generate a docs site and we allow multiple users to add content. It is very easy to unintentionally save a file with wrong BOM configuration.
To reproduce:
Create a Wintersmith site:

C:\Code\> wintersmith new .\test-site
initializing new wintersmith site in C:\Code\test-site using template blog
C:\Code\test-site
+--<EMAIL_ADDRESS>+--<EMAIL_ADDRESS>`--<EMAIL_ADDRESS>done!
preinstall:. -> lifecycle / |#########################################################################--------|

Run wintersmith preview and navigate to the index page and check that the readme article is present:

Next open contents\articles\hello-world\index.md using an editor that can add a BOM char at the beginning of the file. In Notepad++ select Encoding/Convert to UTF-8 and save the file.
Refresh the preview and notice that the README link is missing:

The root cause is that the metadata section is not detected properly since you're reading the first 3 chars of the content looking for "---" (markdown.coffee:123) which in this case is the BOM char.
The naive approach would be to use something like stripBOM() in https://github.com/jonschlinkert/fs-utils, but I don't know if that's enough for all cases?

I don't know either, didn't know BOM was a thing even :) We could modify the regex to allow it, maybe \s matches those chars by default.


More ad domains that aren't blocked

Here's a batch of them, from the family NextDNS configuration.
xad.dnoticias.pt ad.dnoticias.pt data.madovergames.com advert.puzzles.mkjigsaw.com adtracker.mkjigsaw.com

Note: Not sure if data.madovergames.com plays a role regarding game save data or data for a game. Goodbye Ads has blocked it regardless on my personal configuration.

Thanks @CyanoTex.  I added four domains, leaving out data.madovergames.com.
Closing.

Upon further thought, perhaps data.madovergames.com was blocked for a good reason over at Goodbye Ads. Can you add this domain to Unified Hosts?


brozzle-page Not Working With Recent Version of Google Chrome

When I recently used a brozzle-page command with a recent version of Google Chrome, I noticed that brozzler does not load the web page that should be archived.

This results in the web page not being archived successfully.
WARC file: WARCPROX-20230519163909687-00000-0so5t1md.warc

This issue also occurred when trying to archive other web pages:

https://www.tomshardware.com/reviews/nvidia-geforce-rtx-4090-review/3
https://armorgames.com/
https://www.w3schools.com/tags/default.asp
https://www.geeksforgeeks.org/python-classes-and-objects/?ref=lbp
https://mortalkombat.fandom.com/wiki/Tag_Team_Ladder
https://www.youtube.com/watch?v=PZShwWiepeY
https://arquivo.pt/services/complete-page?url=https://pt.ign.com/&timestamp=20220202150304
https://www.bloomberg.com/news/newsletters/2023-01-08/when-will-apple-launch-the-reality-pro-mixed-reality-headset-apple-2023-devices-lcnfzkc7
https://www.theverge.com/23496511/ces-2023-news-products-announcements-tvs-laptops-fitness-trackers

The commands I used are listed below (video example):
warcprox -p 8081 -d ./warcs/IGN/brozzle_page/2023_05_19 --dedup-db-file /dev/null

export BROZZLER_EXTRA_CHROME_ARGS="--ignore-certificate-errors"

brozzle-page --chrome-exe '/usr/bin/google-chrome' --proxy localhost:8081 'https://www.ign.com/articles/the-last-of-us-season-1-review'

A “WebSocketBadStatusException: Handshake status 403 Forbidden” occurred when recently running these commands on Ubuntu (22.04.2 LTS and 20.04.6 LTS) and macOS (Ventura 13.3.1).

When I used these commands earlier this year it was working successfully (video):

After noticing this issue, I went through the recent stable versions of Google Chrome and found the last stable version that worked with the brozzle-page command was version 109.0.5414.119 which was released on January 24, 2023.
chrome.deb URI (109.0.5414.119): https://dl.google.com/linux/chrome/deb/pool/main/g/google-chrome-stable/google-chrome-stable_109.0.5414.119-1_amd64.deb
Crawling session: https://youtu.be/A-zr6zVTZSo?t=5569

Replay session: https://youtu.be/A-zr6zVTZSo?t=6345

The first stable version of Chrome that did not work with the brozzle-page command is version 111.0.5563.110 which was released on March 21, 2023.
chrome.deb URI (111.0.5563.110): https://dl.google.com/linux/chrome/deb/pool/main/g/google-chrome-stable/google-chrome-stable_111.0.5563.110-1_amd64.deb
Crawling session: https://youtu.be/A-zr6zVTZSo?t=4903

Replay session: https://youtu.be/A-zr6zVTZSo?t=4992

Chrome release blog post for 111.0.5563.110: https://chromereleases.googleblog.com/2023/03/stable-channel-update-for-desktop_21.html

Most of the fixed security issues for version 111.0.5563.110 were associated with an attacker creating an HTML page and then exploiting heap corruption:

High CVE-2023-1528: https://nvd.nist.gov/vuln/detail/CVE-2023-1528
High CVE-2023-1530: https://nvd.nist.gov/vuln/detail/CVE-2023-1530
High CVE-2023-1531: https://nvd.nist.gov/vuln/detail/CVE-2023-1531
High CVE-2023-1532: https://nvd.nist.gov/vuln/detail/CVE-2023-1532
High CVE-2023-1533: https://nvd.nist.gov/vuln/detail/CVE-2023-1533
High CVE-2023-1534: https://nvd.nist.gov/vuln/detail/CVE-2023-1534

There was also a security fix that involved internal security work so there was less details for this update to Chrome.

Thank you, @treid003, for your detailed report!
Current brozzler code is compatible with Chrome up to v.110.  This linux version runs without apparent issue:
https://dl.google.com/linux/chrome/deb/pool/main/g/google-chrome-stable/google-chrome-stable_110.0.5481.177-1_amd64.deb
I've also run current code on Apple M1/M2 with Thorium v.110, using the branch here:
https://github.com/internetarchive/brozzler/pull/255


Feature/basic functionality

Initial Image
Crop Image

For some reason, the image is not cropped correctly.

development issue:
If you start up your application and use a circle as customcropshape everything works fine.
If you update it to a square and use hot reload to see your new changes this is the result:

We should take a look at void didUpdateWidget(covariant CustomImageCrop oldWidget); I think the path is not redrawn

The plugin will always use the full width & height. Only take into account the actual space the widget can take up.
(https://github.com/icapps/flutter-custom-image-crop/pull/1/files#diff-36427ab4a1fdca490aa17c986d3e2f197626291632ab97db63993687657d0afeR88) use a layoutbuilder instead

Maybe just one more comment about the file structure. Right now the files are split up between the export file & source files. But we should also split up the source files in different directories to keep the same classes together

models
painters
clippers
widgets


[fr_FR] Ctrl+_ vs Ctrl+8

I'm trying to fix some unit-tests that are currently failing.
In particular, the SwapCharacters test uses the Ctrl+underbar in Emacs mode to perform undo. Although I can fix the test by using an alternate combination of Ctrl+x, Ctrl+u with the same meaning in Emacs and which has the benefit of being more portable, I would like to get to the bottom of this.
The Ctrl+underbar does not work in this particular case with a french keyboard layout. In fact, it seems that this combination sends scan codes more akin to a Ctrl+8 combination.
So I'm not sure how to fix this by editing the KeyInfo-fr-FR-windows.json file or the keybindings in a portable way.
Any hints?
Would it be acceptable to fix the unit-tests by using the more portable key combination ?

Never mind.
I ran the unit-tests incorrectly in a local PowerShell by switching the input language.
The correct way to test it first to swith the input language, and then, launch a new PowerShell window.

GUI applications don't need to restart to handle keyboard layout changes, but console applications may be forced to restart because of a bug in a Win32 api. PSReadLine tests hit that bug.
It's hard to say what the impact of the bug is, but the team responsible for the api is waiting for customer feedback before considering a fix.


Wrong bottom bar positioning

Line 222 calculation is wrong. It should use bottom bar height instead of top bar height:
    bottomBarFrame.origin.y = defaultBottomViewY + topBarHeight;

should be
    bottomBarFrame.origin.y = defaultBottomViewY + self.bottomBarDefaultHeight;

Hi @filipandrei87,
Thanks for pointing this out - I'll get it fixed!

Thanks for reporting @filipandrei87 - this has now been fixed. Will be in the next release.


running coe on linux32 (Ubuntu 16.04 LTS)

Hi,
Following the indications at http://into-cps.github.io/simulation/example.html, i've tried to 3 experiments running co-sim on:

the case study line_follower_robot but the FMUs could not be loaded (see output_follower.txt output_follower.txt)
an example i adapted from another source (the *.mo files i used are in the attachment: springs.zip) for which i generated FMUs with:

jmodelica but i get org.intocps.orchestration.coe.AbortSimulationException: Invalid start condition the instances could not be created in: List({fmu1}.spring1, {fmu2}.spring2) (see output_springs_jmodelica.txt output_springs_jmodelica.txt
); is it that FMUs generated with jmodelica aren't supported?
openmodelica but i get JSON object expected ',' or '}', got: "lineEnd":20,"colSta (see output_springs_omodelica.txt output_springs_omodelica.txt); is it maybe an err in the FMU export from omodelica?

Just for the reference, i attach the json file as well (in the zip
config_springs.json.zip)
Any clue on these issues?
Cheers,
Lacramioara

Hi,
Thanks for reporting this. For the line follower, it could be that the 32bit binaries are missing. @richardpayne  can you look into this?
The jmodelica error does seem to be related to their export. @lausdahl , can you look at this? Would be good to know if we are supporting jmodelica or not.
It would be good to know what version of openmodelica was used. @adrpo can you check if there is indeed a problem?

For the line follower we only have 64bit windows FMUs, I'll make new ones containing Linux/Mac also.
In the case of springs it seems to be a bug in OM generation of support json files containing debug information. I'll have a look.

That's great Adrian. Thanks.

Thanks a lot Luis and Adrian for looking into this!
Indeed, now that i check each of the fmus, LineFollower_Examples_SensorBlock1.fmu & 2 have only windows64 binaries, initially i looked only in the Body_block (which appeared in the error msg) but that one comes with a linux32 binary. Is LineFollower_Examples_SensorBlock1.fmu generated from the mo file from OM_Sensor/LineFollower/Examples?

Yes, the FMUs are generated from those Modelica files.

also, for openmodelica, i generated the FMU with translateModelFMU from OMShell and the version i have is:
OMC version OpenModelica 1.11.0~dev-294-g505e2df

You will also find that the 3Danimation.FMU works in Windows only. There are non-3D multi-model configurations included in the example which omit the 3D view.

Issue:

@adrpo please check that you do not place *.so files for 64 bit under 32 bit. It looks like you do that. See the error wrong ELF class: ELFCLASS64error

There seems to be an issue in the generated FMU. According to the standard this URI is valid: file:/tmp/spring25593247481358409484/resources/ but the FMU complains and requests the authority to be present as well: file:///absolute/path/resources the FMU must support both formats according to FMI 2.0. We know others have challenges respecting that part of the standard too (Modelon FMI Toolbox for Matlab/Simuling) so we added a property you can set until this is fixed: -Dfmi.instantiate.with.empty.authority=true
looks like internal FMU stuff of the one being instantiated. I think Adrian already responded to this

@lausdahl : I just checked all the 32-bit Linux builds for the given error, but the release (1.9.7), stable (1.11.0 beta2), and nightly (1.12.0-dev) all put a proper 32-bit binary in the linux32 directory. The 64-bit version puts files under the linux64 directory.
The cross-compilation translateModelFMU also works properly:
$ file binaries/*/*.so binaries/*/*.dll binaries/*/*.dylib
binaries/arm-linux-gnueabihf/FmuExportCrossCompile.so: ELF 32-bit LSB shared object, ARM, EABI5 version 1 (SYSV), dynamically linked, BuildID[sha1]=d452b0d748a8079718d96aef700d1fb7b7d26cba, not stripped
binaries/linux32/FmuExportCrossCompile.so:             ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, BuildID[sha1]=8f823f3d1e1e17d5bcceb899ca9c0f858b059b37, not stripped
binaries/linux64/FmuExportCrossCompile.so:             ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, BuildID[sha1]=19a4b1f3b099e13575e1a2534a0f820ba7c6d24b, not stripped
binaries/win32/FmuExportCrossCompile.dll:              PE32 executable (DLL) (console) Intel 80386, for MS Windows
binaries/win64/FmuExportCrossCompile.dll:              PE32+ executable (DLL) (console) x86-64, for MS Windows
binaries/darwin32/FmuExportCrossCompile.dylib:         Mach-O i386 dynamically linked shared library, flags:<NOUNDEFS|DYLDLINK|TWOLEVEL|NO_REEXPORTED_DYLIBS>
binaries/darwin64/FmuExportCrossCompile.dylib:         Mach-O 64-bit x86_64 dynamically linked shared library, flags:<NOUNDEFS|DYLDLINK|TWOLEVEL|NO_REEXPORTED_DYLIBS>

If you can reproduce the error in an updated OMC (the given hash is 3 months old of a development branch) of any of the above software channels, I need:

The OS and CPU of the system
The version and source of the binary OMC (running the trusty package, Debian, etc?)
The output of checkSettings() or uname -a (are you running 32-bit OMC on a 64-bit kernel confusing something?)
The commands used to reproduce the error

I'm closing this since no further information has been received. If we get the information then the issue can be re-opened.


Users/yacao/vsmctest

This is the same change that has been reviewed in the original PR and in the release branch PR.


Use lowercase module name when looking up @types packages

New NPM packages can not have uppercase letters in their names. the original package has been shipped already. May be we can make the package lookup in the compiler always look for the lower case name of the type package..
See https://github.com/DefinitelyTyped/DefinitelyTyped/issues/9716#issuecomment-233519331

It appears to already work this way, even with --forceConsistentCasingInFileNames.
My setup:
src/tsconfig.json:
{
  "compilerOptions": {
    "forceConsistentCasingInFileNames": true,
    "outDir": "../out"
  }
}

<EMAIL_ADDRESS>declare const x: number;
export default x;

<EMAIL_ADDRESS>declare namespace Bar {
    const x: number;
}

src/index.ts:
import foo from 'FoO';
foo + 1;

src/foo-user.ts:
import foo from 'FoO';
foo + 1;

src/bar-user.ts:
/// <reference types='BaR'/>
Bar.x;

src/CAPS.ts:
export default 0;

src/caps-user.ts:
// This one really does fail.
import c from 'caps';
c + 1;

There's still a chance that this won't work on a real case-insensitive OS.

The thing that flag does is yell at you if you use uppercase in one place and lowercase in another, so it's unrelated to this AFAIK.

My bad. I guess I'll have to test this out on my linux box.


No valid SAMrecords in FusionDetector

Hi,
Thanks for developing this very useful and much needed tool!
I am running FusionDetector and it seems like it cannot identify any valid SAMrecords in my file.
The command I am running is
java -jar -Xmx72g Jar/Sicelore-2.1.jar FusionDetector I=${sicelore_dir}/passed/fusions/${sample}_clipped_reads.tagbamwithread.US.bam O=${sicelore_dir}/passed/fusions/ PREFIX=fusion CSV=${sicelore_dir}/ValidBarcodes.csv
The output I get is

Thu Feb 23 14:07:02 CET 2023] Executing as a390l@odcf-cn33u24s01 on Linux 3.10.0-1160.76.1.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 14+36-1461; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: null
INFO 2023-02-23 14:07:03 FusionDetector  Cells detected [872103]
INFO 2023-02-23 14:07:04 LongreadParser  start...
INFO 2023-02-23 14:07:26 LongreadParser  Processed           1,000,000 Records.  Elapsed time: 00:00:21s.  Time for last 1,000,000:   21s.  Last read position: chr1:52,481,498
INFO 2023-02-23 14:07:44 LongreadParser  Processed           2,000,000 Records.  Elapsed time: 00:00:39s.  Time for last 1,000,000:   18s.  Last read position: chr1:148,128,006
INFO 2023-02-23 14:08:04 LongreadParser  Processed           3,000,000 Records.  Elapsed time: 00:00:59s.  Time for last 1,000,000:   19s.  Last read position: chr1:212,051,462
INFO 2023-02-23 14:08:24 LongreadParser  Processed           4,000,000 Records.  Elapsed time: 00:01:19s.  Time for last 1,000,000:   20s.  Last read position: chr10:96,750,826
INFO 2023-02-23 14:08:47 LongreadParser  Processed           5,000,000 Records.  Elapsed time: 00:01:42s.  Time for last 1,000,000:   22s.  Last read position: chr11:65,499,045
INFO 2023-02-23 14:09:11 LongreadParser  Processed           6,000,000 Records.  Elapsed time: 00:02:06s.  Time for last 1,000,000:   24s.  Last read position: chr11:85,990,651
INFO 2023-02-23 14:09:32 LongreadParser  Processed           7,000,000 Records.  Elapsed time: 00:02:27s.  Time for last 1,000,000:   21s.  Last read position: chr12:53,386,080
INFO 2023-02-23 14:09:52 LongreadParser  Processed           8,000,000 Records.  Elapsed time: 00:02:47s.  Time for last 1,000,000:   19s.  Last read position: chr13:22,695,871
INFO 2023-02-23 14:10:12 LongreadParser  Processed           9,000,000 Records.  Elapsed time: 00:03:07s.  Time for last 1,000,000:   20s.  Last read position: chr14:68,421,478
INFO 2023-02-23 14:10:32 LongreadParser  Processed          10,000,000 Records.  Elapsed time: 00:03:27s.  Time for last 1,000,000:   20s.  Last read position: chr15:71,164,313
INFO 2023-02-23 14:10:51 LongreadParser  Processed          11,000,000 Records.  Elapsed time: 00:03:46s.  Time for last 1,000,000:   19s.  Last read position: chr16:28,842,788
INFO 2023-02-23 14:11:12 LongreadParser  Processed          12,000,000 Records.  Elapsed time: 00:04:07s.  Time for last 1,000,000:   20s.  Last read position: chr17:17,383,327
INFO 2023-02-23 14:11:30 LongreadParser  Processed          13,000,000 Records.  Elapsed time: 00:04:25s.  Time for last 1,000,000:   18s.  Last read position: chr17:62,016,122
INFO 2023-02-23 14:11:52 LongreadParser  Processed          14,000,000 Records.  Elapsed time: 00:04:47s.  Time for last 1,000,000:   21s.  Last read position: chr19:5,690,296
INFO 2023-02-23 14:12:13 LongreadParser  Processed          15,000,000 Records.  Elapsed time: 00:05:08s.  Time for last 1,000,000:   20s.  Last read position: chr19:46,608,521
INFO 2023-02-23 14:12:34 LongreadParser  Processed          16,000,000 Records.  Elapsed time: 00:05:30s.  Time for last 1,000,000:   21s.  Last read position: chr2:69,770,286
INFO 2023-02-23 14:12:55 LongreadParser  Processed          17,000,000 Records.  Elapsed time: 00:05:50s.  Time for last 1,000,000:   20s.  Last read position: chr2:177,219,081
INFO 2023-02-23 14:13:15 LongreadParser  Processed          18,000,000 Records.  Elapsed time: 00:06:10s.  Time for last 1,000,000:   20s.  Last read position: chr20:31,541,088
INFO 2023-02-23 14:13:34 LongreadParser  Processed          19,000,000 Records.  Elapsed time: 00:06:29s.  Time for last 1,000,000:   18s.  Last read position: chr21:8,437,245
INFO 2023-02-23 14:13:53 LongreadParser  Processed          20,000,000 Records.  Elapsed time: 00:06:48s.  Time for last 1,000,000:   19s.  Last read position: chr22:45,855,782
INFO 2023-02-23 14:14:12 LongreadParser  Processed          21,000,000 Records.  Elapsed time: 00:07:07s.  Time for last 1,000,000:   18s.  Last read position: chr3:56,621,921
INFO 2023-02-23 14:14:34 LongreadParser  Processed          22,000,000 Records.  Elapsed time: 00:07:29s.  Time for last 1,000,000:   22s.  Last read position: chr3:186,789,321
INFO 2023-02-23 14:14:54 LongreadParser  Processed          23,000,000 Records.  Elapsed time: 00:07:49s.  Time for last 1,000,000:   19s.  Last read position: chr4:108,621,949
INFO 2023-02-23 14:15:13 LongreadParser  Processed          24,000,000 Records.  Elapsed time: 00:08:08s.  Time for last 1,000,000:   19s.  Last read position: chr5:64,378,743
INFO 2023-02-23 14:15:34 LongreadParser  Processed          25,000,000 Records.  Elapsed time: 00:08:29s.  Time for last 1,000,000:   20s.  Last read position: chr5:151,662,440
INFO 2023-02-23 14:15:52 LongreadParser  Processed          26,000,000 Records.  Elapsed time: 00:08:47s.  Time for last 1,000,000:   18s.  Last read position: chr6:65,304,141
INFO 2023-02-23 14:16:14 LongreadParser  Processed          27,000,000 Records.  Elapsed time: 00:09:09s.  Time for last 1,000,000:   21s.  Last read position: chr7:15,701,353
INFO 2023-02-23 14:16:33 LongreadParser  Processed          28,000,000 Records.  Elapsed time: 00:09:29s.  Time for last 1,000,000:   19s.  Last read position: chr7:77,736,408
INFO 2023-02-23 14:16:54 LongreadParser  Processed          29,000,000 Records.  Elapsed time: 00:09:50s.  Time for last 1,000,000:   21s.  Last read position: chr7:141,134,916
INFO 2023-02-23 14:17:15 LongreadParser  Processed          30,000,000 Records.  Elapsed time: 00:10:11s.  Time for last 1,000,000:   21s.  Last read position: chr8:118,070,180
INFO 2023-02-23 14:17:34 LongreadParser  Processed          31,000,000 Records.  Elapsed time: 00:10:29s.  Time for last 1,000,000:   18s.  Last read position: chr9:94,293,664
INFO 2023-02-23 14:17:53 LongreadParser  Processed          32,000,000 Records.  Elapsed time: 00:10:48s.  Time for last 1,000,000:   18s.  Last read position: chr12_GL877875v1_alt:158,635
INFO 2023-02-23 14:18:09 LongreadParser  Processed          33,000,000 Records.  Elapsed time: 00:11:04s.  Time for last 1,000,000:   15s.  Last read position: chr12_KI270904v1_alt:23,647
INFO 2023-02-23 14:18:24 LongreadParser  Processed          34,000,000 Records.  Elapsed time: 00:11:19s.  Time for last 1,000,000:   15s.  Last read position: chr6_GL000255v2_alt:3,667,808
INFO 2023-02-23 14:18:43 LongreadParser  Processed          35,000,000 Records.  Elapsed time: 00:11:38s.  Time for last 1,000,000:   18s.  Last read position: chrUn_GL000220v1:153,187
INFO 2023-02-23 14:19:02 LongreadParser  Processed          36,000,000 Records.  Elapsed time: 00:11:57s.  Time for last 1,000,000:   19s.  Last read position: chrX:114,050,215
INFO 2023-02-23 14:19:08 LongreadParser  end...
INFO 2023-02-23 14:19:08 LongreadParser  Total SAMrecords       36341118
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords valid       0
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords unvalid     36341118
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords mapqv=0     0
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords no gene     0
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords no UMI      0
INFO 2023-02-23 14:19:08 LongreadParser  SAMrecords chimeria    0
INFO 2023-02-23 14:19:08 LongreadParser  Total reads            0
INFO 2023-02-23 14:19:08 LongreadParser  Total reads multiSAM   0
INFO 2023-02-23 14:19:08 MoleculeDataset  MoleculeDataset init start...
INFO 2023-02-23 14:19:08 MoleculeDataset  Total molecules               0
INFO 2023-02-23 14:19:08 MoleculeDataset  Total molecule reads  0
INFO 2023-02-23 14:19:08 MoleculeDataset  Total molecule multiIG        0
INFO 2023-02-23 14:19:08 FusionDetector  SetFusions             start...
[Thu Feb 23 14:19:09 CET 2023] org.ipmc.sicelore.programs.FusionDetector done. Elapsed time: 12.10 minutes.
Runtime.totalMemory()=2868903936

The first line of my BAM file looks like-

e80a74fc-6591-435f-9fe7-ad24c506109b_null_CATTCATAGTGTTCCA_AGCCCATACTCC 256     chr1    10522   0       112S120M1D29M3I20M1I1M564N2M2D5M1D5M2I29M1D41M3D25M3I2M1I33M7D28M1D1M2D125M212S *       0       0       *       *       s1:i:270        NM:i:53 AS:i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de:f:0.0793     rl:i:64 cm:i:37 nn:i:0  tp:A:S  ms:i:337 ts:A:+

I suspected it was an issue with the US tag not being added correctly with AddBamReadSequenceTag, but I re-did the tagging with  /NanoporeBC_UMI_finder-2.1.jar tagbamwithread to get the US tags in place. But I still run into this error.
Can you please let me know what might be causing this issue?

Hi,
FusionDetector pipeline has not very maintained in the last version sicelore, there might be some issue in the README.
what i can see is that the bam file is lacking CellBC and UMI tags required for FusionDetector to work correctly so all  SAM records are considered as invalid and the pipeline is not running properly. cellBC and UMI tags are added using AddBamReadTags and it seems not doing the job here. Initially this pipeline was dedicated to be run using the consensus molecules fastq file. Could you give a try to rerun AddBamReadTags using the Sicelore-2.1.220323.jar in github Jar directory  and check the cellBC and UMI tags are present before running FusionDetector. Please also check the .csv file use (FusionDetector Cells detected [872103], do you really have 872k cells in your dataset?)
best,

It works now, thank you so much!


Updated manual; bypass registration code; added a new function QUIT

Hi,
Today I successfully built Corman Lisp from source code using Visual Studio 2005, then I did following things:

Updated manual PDF to reflect the current status of Corman Lisp (GitHub, new MIT license)
Bypassed the registration code when starting Corman Lisp
Added a QUIT lisp function for more convenient use.

I see there's already ASDF with it, so my next step should be porting USOCKET to it, then more and more CL packages should be able to run in it.
Regards,
Chun Tian (binghe)

sorry, it turns out that the Gc.cpp changes are not correct.


OGV Governance Fork test improvement

With the implementation of Oracle Router's recency checks on Oracle prices, our fork test environment no longer processes fork network blocks & time for the amounts configured on the mainnet to pass proposals. We have rather modified the deploy scripts to shorten the proposal voting and queue times.
But this doesn't solve all the issues. Currently, there is a problem with the 060 deploy. The proposal has been submitted on the mainnet and queued. The deploy scripts rightly shorten the voting and queue time on the contract but the proposal has already been queued on the mainnet before the queue time has been shortened on the forked environment based off of the mainnet.
Possible solutions:

find a hackish way by modifying storage slots to change the queue time of an active proposal
cancel queued proposal and re-submit it, vote for it and queue & execute it
alter Oracle router so that on the forked network the data can be stale and tests will pass. -> can't really test oracle data recency then

I'd vote for option 2.

I agree with option 2. Thanks @sparrowDom


[FEAT] - Use Case: RBAC Hierarchy

Priority
None
Description
In our current way of deploying k8s we have a lot of cluster where parts of the cluster ( the api, etcd etc. ) run in one cluster (mgmt) and the workload runs in another (workload).
Not only do i want to register the workload cluster in greenhouse and the management cluster. I want to be able to assign RBAC permissions towards a namespace in mgmt as well as the workload cluster.
E.g.: in our ceph use case we have a support team that needs to be admin inside the ceph clusters and able to manipulate CRD's and k8s primitives in one namespace of the mgmt cluster.
Reference Issues
No response

i think it is still a valid usecase

still no dice :(


Removing ticks in a graph scene

What is the best way to remove all the ticks on the axes?
I removed ticks by doing this:
class Function(GraphScene):
    CONFIG = {
    "x_min": -5,
    "x_max": 5,
    "y_min": -3,
    "y_max": 3,
    }
    def construct(self):
        self.x_leftmost_tick = self.x_max+1
        self.y_bottom_tick = self.y_max+1

        self.setup_axes(animate = True)
        self.wait(3)

But doing this causes the x-axis label to appear at the origin, like so:

To keep the x-label at it's usual position by default, in line 89 of manimlib/scene/graph_scene.py, I replaced
x_axis.get_tick_marks(), UP + RIGHT,
by
x_axis.get_corner(UP + RIGHT), UP + RIGHT,
The y-axis label has a configuration similiar to the above line. Shouldn't that be the configuration for the x-axis label's position by default?

spent some time digging the source code.
The ticks are constructed with NumberLine class, the CONFIG in the NumberLine has a boolean value include_ticks, which defaults to True. You can monkey patch the CONFIG to turn the value to False.
when the boolean is set to false, this line, which sets up the tick_marks variable, does not get executed.
    if self.include_ticks:
        self.add_tick_marks()

However, the other method get_tick_marks expects tick_marks to be present. This method is called when GraphScene calls setup_axes
    if self.x_axis_label:
        x_label = TextMobject(self.x_axis_label)
        x_label.next_to(
            x_axis.get_tick_marks(), UP + RIGHT,
            buff=SMALL_BUFF
        )
        x_label.shift_onto_screen()
        x_axis.add(x_label)
        self.x_axis_label_mob = x_label

which will also be executed if you want to have the x axis label. The y axis label uses get_corner which is what you did.
The code is not setup to handle no tick cases :(
Here is the code for monkey patching the CONFIG
CUSTOM_CONFIG = {
    "color": LIGHT_GREY,
    "x_min": -FRAME_X_RADIUS,
    "x_max": FRAME_X_RADIUS,
    "unit_size": 1,
    "include_ticks": False,  # this boolean controls tick generation
    "tick_size": 0.1,
    "tick_frequency": 1,
    # Defaults to value near x_min s.t. 0 is a tick
    # TODO, rename this
    "leftmost_tick": None,
    # Change name
    "numbers_with_elongated_ticks": [0],
    "include_numbers": False,
    "numbers_to_show": None,
    "longer_tick_multiple": 2,
    "number_at_center": 0,
    "number_scale_val": 0.75,
    "label_direction": DOWN,
    "line_to_number_buff": MED_SMALL_BUFF,
    "include_tip": False,
    "tip_width": 0.25,
    "tip_height": 0.25,
    "decimal_number_config": {"num_decimal_places": 0},
    "exclude_zero_from_default_numbers": False,
}

NumberLine.CONFIG = CUSTOM_CONFIG
# NumberLine.get_tick_marks = None


Write config file atomically

Description of the Change
We (the Nuclide team) continue to have reports of #17060 from Windows users, even after #17166. The cause isn't certain, however, we do know that the before-quit event isn't reliable on Windows. In any case, atomic writes (write + move) are less error-prone.
I rolled back the fix from #17060 to get back to a state where the issue could be reproduced somewhat reliably, then made the change an was unable to repro. This isn't a guaranteed fix (since the same could be said about #17060), but it seems more robust.
I was initially worried about the watcher not picking up the replace, but I tested that file updates were reflected in UI and that UI updates were mirrored to the file on both MacOS and Windows and we're good.
Alternate Designs
None.
Possible Drawbacks

We're doing two operations (write and move) where we used to do one so this is going to be slower.
There could be something subtle with the watcher I didn't pick up on when testing.
I haven't verified on Linux.

Verification Process

For both MacOS and Windows:

Update editor.fontSize in my config.cson and see change in Atom.
Use ⌘+ to increase the font size and see change in config.cson.

Install @Arcanemagus's settings-wiper from #17060 and repeat his instructions in that issue for wiping settings many (~50) times without settings loss.

Applicable Issues

#17166
#17060
#16786
#14909

cc @ebluestein

Thanks @matthewwithanm!

FYI: We unfortunately ran into an issue (#18118) with this change after rolling it out in Atom 1.31.0 and 1.32.0-beta0. As a result, we had to revert this change in https://github.com/atom/atom/pull/18134.


Provide types for exposed components

Define types for the components exposed in index.ts for safety and better integration with linters.

@miguelgrc hi there, please assign this to me, i would like to fix this, thanks

@Sky-De we've merged #43 :)

@miguelgrc thanks for informing me, I will start adding types to
1.PropertyEditor
2.SelectFieldType
3.SchemaPreview
4.FormPreview
5.SelectOrEdit
components as clean as possible, but these days I'm a little busy, every day I will work on one of them, and after they are all done I will create PR

@miguelgrc Hey again, I need your help, if you don't mind. First of all, I encountered this warning which prevents the app from loading:

then can you please clarify store/schrmaWizard types
const initialState = {
current: {
schema: {},
uiSchema: {},
},
initial: {
schema: {},
uiSchema: {},
},
initialConfig: {},
config: {},
field: {},
formData: {},
propKeyEditor: null,
error: null,
loader: false,
version: null,
};
you have used { } empty objects instead of the initial value inside those objects which makes it hard to understand what exactly those types should be
also const path = useSelector((state) => state.schemaWizard.field.path);  schemaWizard is not part of state, what is that ?
and last question does this app work?


fix opening sentence

first of several more changes.

Yes, in adoptions that was a typo--should be clicking "on." I usually print
a hardcopy to proof before finalizing. With the printer being out of toner
indefinitely, I had to proof onscreen only. I proofread better when I have
it on paper in front of me.
I'll clean up the other typos you found. Thanks for giving it a careful
read.
On the News section...yeah...I don't think it would hurt to link to the
slides or the video there..
Lois
On Mon, Apr 2, 2018 at 2:29 PM, Vladimir Diaz<EMAIL_ADDRESS>wrote:

@vladimir-v-diaz commented on this pull request.
In adoptions.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178609334
:

@@ -5,7 +5,8 @@ css_id: adoptions

Adoptions
-(Many of the images below link to articles that cover the TUF adoption.)
+By clicking of the images below, you can link to articles that cover the TUF
"By clicking of the images below, ..."
Is there a typo here?
In news.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178610602
:

@@ -66,32 +66,32 @@ please see [TUF Augmentation Proposals
Riyaz Faizullabhoy from Docker gave a
talk
on TUF and Notary at LinuxCon North America.  Slides of his talk are available
-here:
-https://events.linuxfoundation.org/events/linuxcon-north-america/program/slides
+here.

+March 18, 2016
+
+>
+Trishank Kuppusamy presents "Diplomat: Using Delegations to Protect Community
+Repositories" at NSDI 2016.
Should we link to the page that contains the presentation slides, audio
recording, paper, etc.?
https://www.usenix.org/node/194973
In overview.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178611368
:

@@ -21,8 +21,7 @@ growing flow of updates has also created a need for better
ways to protect the systems that manage them. Though a number of strategies have
been introduced and used over the last decade or so to enhance the
authenticity—and by extension, the security of update systems—most have drawbacks
-that have left update files and the repositories that host them.
-vulnerable to a number of attacks.
+that have left update files and the repositories that host them s,vulnerable to a number of attacks.

typo: " ... that host them s, ..."
In overview.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178611615
:

@@ -73,18 +72,18 @@ account, such as when:
there is an update.

An attacker gives you an older, insecure version of a file that you

already have, so you download it and blindly use it thinking it's
newer.

already have and tricks you into thinking it's
newer. You download it an dblindly use it.

typo: "... dblindly ..."
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#pullrequestreview-108692516,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AN5qX7wd5_hNjKkSqSrXNRHS2T50pQwSks5tkm3ugaJpZM4TCE6B
.

Two more things I noticed when I was checking through the web site for data
for a revision on Wikipedia...First off, we mentioned the two PEPs but I
could find no link to these two documents. If we don't want to link to
these texts through the publications list, can we embed a link on the
Timeline where they are mentioned?
Second, on the new publications page, the links for the last two items: A
Look In the Mirror: Attacks on Package Managers
https://theupdateframework.github.io/papers/package-management-security-tr08-02.pdf?raw=true
Package Management Security
https://theupdateframework.github.io/papers/attacks-on-package-managers-ccs2008.pdf?raw=true
are reversed.
I can fix these when I go in to correct the other typos you found if you
let me know where you want the PEPs.
Lois
On Mon, Apr 2, 2018 at 2:34 PM, Lois A DeLong<EMAIL_ADDRESS>wrote:

Yes, in adoptions that was a typo--should be clicking "on." I usually
print a hardcopy to proof before finalizing. With the printer being out of
toner indefinitely, I had to proof onscreen only. I proofread better when I
have it on paper in front of me.
I'll clean up the other typos you found. Thanks for giving it a careful
read.
On the News section...yeah...I don't think it would hurt to link to the
slides or the video there..
Lois
On Mon, Apr 2, 2018 at 2:29 PM, Vladimir Diaz<EMAIL_ADDRESS>wrote:

@vladimir-v-diaz commented on this pull request.
In adoptions.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178609334
:

@@ -5,7 +5,8 @@ css_id: adoptions

Adoptions
-(Many of the images below link to articles that cover the TUF adoption.)
+By clicking of the images below, you can link to articles that cover the TUF
"By clicking of the images below, ..."
Is there a typo here?
In news.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178610602
:

@@ -66,32 +66,32 @@ please see [TUF Augmentation Proposals
Riyaz Faizullabhoy from Docker gave a
talk
on TUF and Notary at LinuxCon North America.  Slides of his talk are available
-here:
-https://events.linuxfoundation.org/events/linuxcon-north-america/program/slides
+here.

+March 18, 2016
+
+>
+Trishank Kuppusamy presents "Diplomat: Using Delegations to Protect Community
+Repositories" at NSDI 2016.
Should we link to the page that contains the presentation slides, audio
recording, paper, etc.?
https://www.usenix.org/node/194973
In overview.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178611368
:

@@ -21,8 +21,7 @@ growing flow of updates has also created a need for better
ways to protect the systems that manage them. Though a number of strategies have
been introduced and used over the last decade or so to enhance the
authenticity—and by extension, the security of update systems—most have drawbacks
-that have left update files and the repositories that host them.
-vulnerable to a number of attacks.
+that have left update files and the repositories that host them s,vulnerable to a number of attacks.

typo: " ... that host them s, ..."
In overview.md
https://github.com/theupdateframework/theupdateframework.github.io/pull/32#discussion_r178611615
:

@@ -73,18 +72,18 @@ account, such as when:
there is an update.

An attacker gives you an older, insecure version of a file that you

already have, so you download it and blindly use it thinking it's
newer.

already have and tricks you into thinking it's
newer. You download it an dblindly use it.

typo: "... dblindly ..."
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You are receiving this because you authored the thread.
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The PEP can be found here:
https://www.python.org/dev/peps/pep-0458/
https://www.python.org/dev/peps/pep-0480/
There isn't a single document for each PEP, so we'll have to link to them from our website.  More recent versions of the PEPs are under revision control on the interoperability repo.
https://github.com/pypa/interoperability-peps/blob/master/pep-0458-tuf-online-keys.rst

I honestly don't remember but I'm pretty sure I didn't address your
comments. I've been pretty deeply immersed in another project the last
two weeks. I will look on Monday and address all your comments then.
Thanks for the reminder and I apologize for the delay.
Lois
On Fri, Apr 13, 2018 at 02:18 PM, Vladimir Diaz wrote:
@jhdalek55 https://github.com/jhdalek55  Is this a work in progress?
I'm not sure if you addressed my comments (and haven't pushed them yet),
or you still need more time.
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Thanks!  Looks good to me, I only made a small change to the headings.


Flutter Support

Currently, most of the platforms are supported for core. Adding flutter support would extend the library's UI support for many platforms, with a single Dart codebase.

You have a flutter label now, no pressure 😆

Flutter's MethodChannel APIs only support primitive and basic types yet, so it's not possible to integrate core without porting it to dart.


Added dart tags for better code readability

The dart tags were missing so I added them for better readability

thanks .
Has been changed, it is not convenient to merge, but has been modified


feat: new deploys params for ERC20 approve and transfer

This PR provides two new deploy parameters and two new deploy results to support ERC20 tokens approve and transfer operations.

Codecov Report

Merging #7 (a81103a) into main (705c28f) will decrease coverage by 0.86%.
The diff coverage is 71.42%.

@@            Coverage Diff             @@
##             main       #7      +/-   ##
==========================================
- Coverage   85.97%   85.10%   -0.87%
==========================================
  Files          14       16       +2
  Lines         221      235      +14
  Branches       32       34       +2
==========================================
+ Hits          190      200      +10
- Misses         28       32       +4
  Partials        3        3

Impacted Files
Coverage Δ

src/services/deploys/erc20/actions/erc20Approve.js
71.42% <71.42%> (ø)

...rc/services/deploys/erc20/actions/erc20Transfer.js
71.42% <71.42%> (ø)

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LGTM thx


Meetups List Link

I recently learned about https://www.vuemeetups.org/.
It might be helpful to the community if this were listed on the website menu.
It might fit under the Ecosystem tab > Help section.
Just an idea.
Thanks for your time, and definately thanks for vue.

I like that! PR welcome. 🙂

Thanks for this!


How to correctly restore navigation stack with temporary router?

I have an issue with state restoration and temporarty router.
Here are my routes:
class AppRoutes {
  static List<QRoute> bottomSheetRoutes = [
    QRoute(
        name: bottomSheetExamplePageName,
        path: bottomSheetExamplePagePath,
        builder: () => const BottomSheetExamplePage(),
    ),
  ];
  final routes = [
    QRoute(
        name: homePageName,
        path: homePagePath,
        pageType: const QPlatformPage(restorationId: homePageName),
        builder: () => const HomePage(),
        children: [
          ...bottomSheetRoutes,
        ],
  ];
}

I want to show bottom sheet over the home page with temporary router and call this method on HomePage:
    showModalBottomSheet(
      context: context,
      builder: (_) => TemporaryQRouter(
        path: '/temp_router',
        initPath: bottomSheetExamplePagePath,
        routes: AppRoutes.bottomSheetRoutes,
      ),
    );

The steps are the following:

Enable "Don't keep activities" option on Android device.
Open the app, from home page call showModalBottomSheet method.
Put the app to background, so that the system kills its process.
Return to the app, so that its state and route are restored.
Expected result: the app is opened on the home page, the current path is '/home'
Actual result: the app shows "Page not found', the current path is '/temp_router/bottom_sheet_example'

Is there a way to have the expected result?

Temporary router does not support state restoration yet


Add randomly generates container names

As the name says. Now we have usable shortnames.

LGTM

Flake talking to the registry

bot, retest this please

@rh-atomic-bot r+


Fixed the broken links in semisupervised_simclr.py

Fixed the broken links  of RandomTranslation and RandomZoom Layers in semisupervised_simclr.py

Can you please make these changes in .ipynb and .md files as well?

@sachinprasadhs,
Changes have been performed in both .md and .ipynb files. Thank you!


Fixed linters warnings, add gomodules support, function optimization

Updated travis to support go 1.13
Updated tests (errors handling, simplify)
Add go modules support
Optimize pack function

Coverage increased (+0.2%) to 49.24% when pulling 9b23ad54ac18ab47dfa77122ec8dcbcfa59be740 on ValeryPiashchynski:Fixed_linter_warnings_optimize_pack_function into 8d98395348c70fe3b6313077aad9ca7f8ead54b8 on spiral:master.

Coverage increased (+0.09%) to 49.148% when pulling 9b23ad54ac18ab47dfa77122ec8dcbcfa59be740 on ValeryPiashchynski:Fixed_linter_warnings_optimize_pack_function into 8d98395348c70fe3b6313077aad9ca7f8ead54b8 on spiral:master.

Coverage increased (+0.2%) to 49.24% when pulling 9b23ad54ac18ab47dfa77122ec8dcbcfa59be740 on ValeryPiashchynski:Fixed_linter_warnings_optimize_pack_function into 8d98395348c70fe3b6313077aad9ca7f8ead54b8 on spiral:master.


404 at: /v1.8/introduction/understanding-docker/

URL: /v1.8/introduction/understanding-docker/

404 in archive version.

The correct URL is https://docs.docker.com/v1.8/engine/introduction/understanding-docker/, FYI.

Closed via #2787


Added new source

from BlackSnowDot/proxylist-update-every-minute/

good source have lot of good proxies

Only 0.7% of the proxies in this source work, at least for me. This is very inefficient.


Improvements to .emote.

You see, I was fairly confused with the way .emote worked. In my opinion, removing spaces should be completely optional, instead of making no spaces between emotes the default.
So, hereby, - now removes the space between emotes, + still adds a \n, and _ still adds a \u200b. No other changes were made.
And also, since I ripped the code from CCBot's emote command, the extensibility of the formatting function is now, in my opinion, much easier.

And also, since I ripped the code from CCBot's emote command,

Credit where credit is due. I don't want to repeat the events of Re-Jill.

I would personally prefer to keep the current behavior of - (adding a space, not removing a space).

This seems counter intuitive to me. Why should emotes be stitched together by default?

I feel it makes less sense for one to type a character in an emote call that is meant to actually remove a character. It feels backwards.
Having spaces be manually specified just makes more sense, in my opinion.

Aren't you already typing a space between emotes in the invocation? Why would you want to specify the space again as another character to actually add it to the output?

I would agree with that only if spaces were significant - i.e. putting 3 spaces between two emotes names would result in the message having 3 spaces between the two emotes, and not just 1 space. Using - as a space adder, and not remover also allows one to do multiple spaces between emotes much more intuitively if one desired.

I would agree with that only if spaces were significant

My final say on this PR will be that readability is significant enough. Stitched emotes look bad.
I will await the proper review before wasting more words on this.


Issue #1611: Fix path issue with DetektTaskDslTest

macOS puts various temporary directories into a separate mount
point, and then creates symlinks from the more-traditional
POSIX layout locations to the separate mount point. This change
uses canonicalPath instead of absolutePath to align the
expected locations with what happens during shell expansion.
This might also address #1616.

I haven't tried this on any other platforms yet. Are there supported platforms that aren't tested in the CI pipeline?

FYI, the Java 8 build worked, but the Java 11 and Java 12 builds failed while installing the JVM. Looks like a systemic issue.

Are there supported platforms that aren't tested in the CI pipeline?

It's tested in CI on Linux (via Travis) and Windows (via AppVeyor), and we'll look to introduce testing on macOS on Travis as well since there are differences on that platform that have been identified. Thanks for the quick fix!


⚠ Bofrost.at has degraded performance

In cdf1931, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1202 ms

Resolved: Bofrost.at performance has improved in caebf4b.


python310Packages.onvif-zeep-async: 1.2.1 -> 1.2.2

Description of changes

Things done

Built on platform(s)

[ ] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
23.05 Release Notes (or backporting 22.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[ ] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 223125 run on x86_64-linux 1

5 packages built:

home-assistant-component-tests.onvif
python310Packages.onvif-zeep-async
python310Packages.onvif-zeep-async.dist
python311Packages.onvif-zeep-async
python311Packages.onvif-zeep-async.dist


Script must be in current directory

If I want to use my own command script and run it like 'uuu script.uu', it works fine.
If I do 'uuu scripts/script.uu', it fails because it adds 'scripts/' to every pathname in the script.
For example, my script includes this line:

boot -f /projects/yocto/build/tmp/deploy/images/sabre/u-boot.imx

When I run 'uuu scripts/script.uu', I get this message:

Error: fail open file: >scripts//projects/yocto/build/tmp/deploy/images/sabre/u-boot.imx

The location of the script should not cause any changes to the paths in the script. That could lead to very confusing behaviour if ended up as a valid, but wrong filename

all file support related to uuu script. If you want to use absolute path, please add > before path

if still have problem, please reopen.


update CHANGES.md release notes to reflect delay in package release

Description
Due to release delay, a few more PRs were merged before the pypi release was completed.
Hence, this PR updates the CHANGES.md release notes to reflect delay in 0.20.0 package release.
Checklist

[ ] I have added screenshots above for all UI changes.
[ ] I have added e2e tests for all UI changes.
[x] Documentation was updated if it was needed.

Codecov Report

Merging #1581 (d3ac128) into main (e3d0f24) will decrease coverage by 4.31%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1581      +/-   ##
==========================================
- Coverage   88.04%   83.73%   -4.32%
==========================================
  Files         109       22      -87
  Lines        5295      418    -4877
==========================================
- Hits         4662      350    -4312
+ Misses        633       68     -565

Flag
Coverage Δ

unittests
83.73% <ø> (-4.32%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files
Coverage Δ

erroranalysis/erroranalysis/_internal/constants.py

raiwidgets/raiwidgets/dashboard.py

responsibleai/responsibleai/__init__.py

.../databalanceanalysis/aggregate_balance_measures.py

responsibleai/responsibleai/_config/__init__.py

...eai/responsibleai/managers/data_balance_manager.py

...is/erroranalysis/_internal/surrogate_error_tree.py

...ibleai/_tools/shared/state_directory_management.py

...iwidgets/raiwidgets/model_performance_dashboard.py

erroranalysis/erroranalysis/version.py

... and 77 more

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Hyperband bracket generation is inconsistent with the original Hyperband paper

The BOHB paper says that each SH bracket samples $n = \lceil \frac{s_{\max} + 1}{s + 1} \eta^s \rceil$ configurations; however, this line samples $n = \lfloor\lfloor \frac{s_{\max} + 1}{s + 1} \rfloor \eta^s\rfloor$ configurations.
In reality, this line should be:
n0 = int(np.ceil(self.max_SH_iter / (s + 1) * self.eta ** s))

Note that self.max_SH_iter is $s_{\max} + 1$.

This repo is no longer maintained.


No module named 'djangosaml2idp'

I tried to run docker-compose up for the example setup but i get this error:

djangosaml2idp_idp exited with code 1
djangosaml2idp_idp | Traceback (most recent call last):
djangosaml2idp_idp |   File "manage.py", line 22, in
djangosaml2idp_idp |     execute_from_command_line(sys.argv)
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/site-packages/django/core/management/init.py", line 381, in execute_from_command_line
djangosaml2idp_idp |     utility.execute()
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/site-packages/django/core/management/init.py", line 357, in execute
djangosaml2idp_idp |     django.setup()
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/site-packages/django/init.py", line 24, in setup
djangosaml2idp_idp |     apps.populate(settings.INSTALLED_APPS)
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/site-packages/django/apps/registry.py", line 91, in populate
djangosaml2idp_idp |     app_config = AppConfig.create(entry)
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/site-packages/django/apps/config.py", line 90, in create
djangosaml2idp_idp |     module = import_module(entry)
djangosaml2idp_idp |   File "/usr/local/lib/python3.6/importlib/init.py", line 126, in import_module
djangosaml2idp_idp |     return _bootstrap._gcd_import(name[level:], package, level)
djangosaml2idp_idp |   File "", line 994, in _gcd_import
djangosaml2idp_idp |   File "", line 971, in _find_and_load
djangosaml2idp_idp |   File "", line 953, in _find_and_load_unlocked
djangosaml2idp_idp | ModuleNotFoundError: No module named 'djangosaml2idp'

This was due to a symlink between the example setup and the package python code, which didn't mount correctly in Docker, so the source code for that application could not be found. It has been updated (the base image has been updated as well in the linked MR but that is not relevant for this issue), and works again (confirmed by me that it works locally and the login flow is succesful)


Removing Microsoft.AspNetCore.Mvc.Razor.RazorViewEngineOptions --> AdditionalCompilationReferences will block us

Related to #4902
In https://github.com/simplcommerce/SimplCommerce, we apply modular architecture, each module is a Razor Class Library. We manually load modules and then add them to the main web app using ApplicationPart. We also support theming, users can switch between the themes at run time. This feature requires run time compilation of cshtml files.
Currently it works fine. But if you remove the api for adding AdditionalCompilationReferences on RazorViewEngineOptions it will not work.
I have create a simple project to show this issue here https://github.com/thiennn/plugin2_2.

@thiennn MVC uses deps files to determine the location of compilation references. The plugin assembly that you load has a deps file but with PreserveCompilationContext disabled. Consequently it results in MVC determining that there are no references to be loaded from it. A couple of ways for you to fix it:

Use a regular P2P reference between your app and the plugin. It'll ensure that your app has the correct closure of references when attempting to runtime compile views. This would be my recommended solution.
Alternatively, ensure a deps file does not exist next to the plugin assembly. Targeting netstandard2.0, using <GenerateDependencyFile>false</GenerateDependencyFile>, or just deleting it as a post build step are all possible ways to go about this.

Thank @pranavkm Option 1 will prevent the ability to add plugins at run-time. Deleting the deps file seems the suitable workaround for us at this moment.

Closing since the question has been answered.