HDFS-17444. Add getJournalSyncerStarted jmx metrics, to Indicates whether the JournalSyncer thread has been started.

The JornalNode JVM process is not immediately in a normal state until the JournalSyncer thread is started.
For some management platforms such as Ambari rolling restart JournalNode, we need a jmx metric to determine whether the JournalSyncer thread is started and enter working state for current namespace before restarting the next JournalNode. Otherwise, restart too quickly and more than half of JournalNodes will be out of order, causing the NameNode to die.
When i add it , the effect is as follows:

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_ trunk Compile Tests _

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1m 22s

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1m 16s

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1m 24s

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1m  7s

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+1 :green_heart:
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1m 48s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

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35m 51s

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_ Patch Compile Tests _

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1m 14s

the patch passed

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1m 12s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
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1m 12s

the patch passed

+1 :green_heart:
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1m  9s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
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1m  9s

the patch passed

+1 :green_heart:
blanks
0m  0s

The patch has no blanks issues.

+1 :green_heart:
checkstyle
0m 57s

the patch passed

+1 :green_heart:
mvnsite
1m 13s

the patch passed

+1 :green_heart:
javadoc
0m 53s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m 34s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
3m 18s

the patch passed

+1 :green_heart:
shadedclient
35m 34s

patch has no errors when building and testing our client artifacts.

_ Other Tests _

+1 :green_heart:
unit
277m  7s

hadoop-hdfs in the patch passed.

+1 :green_heart:
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0m 46s

The patch does not generate ASF License warnings.

435m 18s

Subsystem
Report/Notes

Docker
ClientAPI=1.45 ServerAPI=1.45 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/1/artifact/out/Dockerfile

GITHUB PR
https://github.com/apache/hadoop/pull/6694

Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell detsecrets

uname
Linux f39efc4d7bd8 5.15.0-94-generic #104-Ubuntu SMP Tue Jan 9 15:25:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Build tool
maven

Personality
dev-support/bin/hadoop.sh

git revision
trunk / 2efc09ba67e36eddf303e10d0034d2f33c348fd6

Default Java
Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Multi-JDK versions
/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Test Results
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/1/testReport/

Max. process+thread count
3500 (vs. ulimit of 5500)

modules
C: hadoop-hdfs-project/hadoop-hdfs U: hadoop-hdfs-project/hadoop-hdfs

Console output
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/1/console

versions
git=2.25.1 maven=3.6.3 spotbugs=4.2.2

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17m 21s

Docker mode activated.

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The patch does not contain any @author tags.

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The patch appears to include 1 new or modified test files.

_ trunk Compile Tests _

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44m 12s

trunk passed

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1m 20s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
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1m 17s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

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1m 11s

trunk passed

+1 :green_heart:
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1m 25s

trunk passed

+1 :green_heart:
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1m  9s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m 43s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

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3m 12s

trunk passed

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35m 54s

branch has no errors when building and testing our client artifacts.

_ Patch Compile Tests _

+1 :green_heart:
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1m 12s

the patch passed

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1m 14s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javac
1m 14s

the patch passed

+1 :green_heart:
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1m  7s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
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1m  7s

the patch passed

+1 :green_heart:
blanks
0m  0s

The patch has no blanks issues.

+1 :green_heart:
checkstyle
0m 58s

the patch passed

+1 :green_heart:
mvnsite
1m 13s

the patch passed

+1 :green_heart:
javadoc
0m 54s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m 34s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
3m 16s

the patch passed

+1 :green_heart:
shadedclient
35m 47s

patch has no errors when building and testing our client artifacts.

_ Other Tests _

+1 :green_heart:
unit
273m 52s

hadoop-hdfs in the patch passed.

+1 :green_heart:
asflicense
0m 46s

The patch does not generate ASF License warnings.

431m 54s

Subsystem
Report/Notes

Docker
ClientAPI=1.45 ServerAPI=1.45 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/2/artifact/out/Dockerfile

GITHUB PR
https://github.com/apache/hadoop/pull/6694

Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell detsecrets

uname
Linux b37458ff93e5 5.15.0-94-generic #104-Ubuntu SMP Tue Jan 9 15:25:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Build tool
maven

Personality
dev-support/bin/hadoop.sh

git revision
trunk / 8d0ef9a8fc6f24bd559f5c3e10b0b34aa16ab7c6

Default Java
Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Multi-JDK versions
/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Test Results
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/2/testReport/

Max. process+thread count
3148 (vs. ulimit of 5500)

modules
C: hadoop-hdfs-project/hadoop-hdfs U: hadoop-hdfs-project/hadoop-hdfs

Console output
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/2/console

versions
git=2.25.1 maven=3.6.3 spotbugs=4.2.2

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@hiwangzhihui, Hi~, please help me review it.

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+0 :ok:
reexec
6m 44s

Docker mode activated.

_ Prechecks _

+1 :green_heart:
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+0 :ok:
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_ trunk Compile Tests _

+1 :green_heart:
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33m 35s

trunk passed

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0m 40s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

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0m 37s

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0m 36s

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0m 42s

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0m 39s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
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1m  8s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
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1m 49s

trunk passed

+1 :green_heart:
shadedclient
22m 47s

branch has no errors when building and testing our client artifacts.

_ Patch Compile Tests _

+1 :green_heart:
mvninstall
0m 36s

the patch passed

+1 :green_heart:
compile
0m 37s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javac
0m 37s

the patch passed

+1 :green_heart:
compile
0m 34s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
javac
0m 34s

the patch passed

+1 :green_heart:
blanks
0m  1s

The patch has no blanks issues.

+1 :green_heart:
checkstyle
0m 28s

the patch passed

+1 :green_heart:
mvnsite
0m 37s

the patch passed

+1 :green_heart:
javadoc
0m 29s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
0m 58s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
1m 57s

the patch passed

+1 :green_heart:
shadedclient
23m 47s

patch has no errors when building and testing our client artifacts.

_ Other Tests _

-1 :x:
unit
199m 12s
/patch-unit-hadoop-hdfs-project_hadoop-hdfs.txt
hadoop-hdfs in the patch passed.

+1 :green_heart:
asflicense
0m 32s

The patch does not generate ASF License warnings.

299m 50s

Reason
Tests

Failed junit tests
hadoop.hdfs.tools.TestDFSAdmin

Subsystem
Report/Notes

Docker
ClientAPI=1.45 ServerAPI=1.45 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/4/artifact/out/Dockerfile

GITHUB PR
https://github.com/apache/hadoop/pull/6694

Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell detsecrets

uname
Linux 5a1da249503d 5.15.0-94-generic #104-Ubuntu SMP Tue Jan 9 15:25:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Build tool
maven

Personality
dev-support/bin/hadoop.sh

git revision
trunk / 47bfef529f5f69a1ae5d0f2b430df35648c47deb

Default Java
Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Multi-JDK versions
/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Test Results
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/4/testReport/

Max. process+thread count
4236 (vs. ulimit of 5500)

modules
C: hadoop-hdfs-project/hadoop-hdfs U: hadoop-hdfs-project/hadoop-hdfs

Console output
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/4/console

versions
git=2.25.1 maven=3.6.3 spotbugs=4.2.2

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:broken_heart: -1 overall

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+0 :ok:
reexec
0m 19s

Docker mode activated.

_ Prechecks _

+1 :green_heart:
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0m  0s

No case conflicting files found.

+0 :ok:
codespell
0m  0s

codespell was not available.

+0 :ok:
detsecrets
0m  0s

detect-secrets was not available.

+1 :green_heart:
@author
0m  0s

The patch does not contain any @author tags.

+1 :green_heart:
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0m  0s

The patch appears to include 1 new or modified test files.

_ trunk Compile Tests _

+1 :green_heart:
mvninstall
34m 52s

trunk passed

+1 :green_heart:
compile
0m 47s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
compile
0m 41s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
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0m 43s

trunk passed

+1 :green_heart:
mvnsite
0m 43s

trunk passed

+1 :green_heart:
javadoc
0m 42s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m  8s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
1m 43s

trunk passed

+1 :green_heart:
shadedclient
23m 14s

branch has no errors when building and testing our client artifacts.

_ Patch Compile Tests _

+1 :green_heart:
mvninstall
0m 42s

the patch passed

+1 :green_heart:
compile
0m 41s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javac
0m 41s

the patch passed

+1 :green_heart:
compile
0m 39s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
javac
0m 39s

the patch passed

+1 :green_heart:
blanks
0m  0s

The patch has no blanks issues.

+1 :green_heart:
checkstyle
0m 33s

the patch passed

+1 :green_heart:
mvnsite
0m 47s

the patch passed

+1 :green_heart:
javadoc
0m 32s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m  4s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
1m 52s

the patch passed

+1 :green_heart:
shadedclient
26m 17s

patch has no errors when building and testing our client artifacts.

_ Other Tests _

-1 :x:
unit
201m 16s
/patch-unit-hadoop-hdfs-project_hadoop-hdfs.txt
hadoop-hdfs in the patch passed.

+1 :green_heart:
asflicense
0m 32s

The patch does not generate ASF License warnings.

301m 10s

Reason
Tests

Failed junit tests
hadoop.hdfs.server.namenode.TestAddStripedBlocks

Subsystem
Report/Notes

Docker
ClientAPI=1.45 ServerAPI=1.45 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/5/artifact/out/Dockerfile

GITHUB PR
https://github.com/apache/hadoop/pull/6694

Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell detsecrets

uname
Linux 8dee1c44b678 5.15.0-94-generic #104-Ubuntu SMP Tue Jan 9 15:25:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Build tool
maven

Personality
dev-support/bin/hadoop.sh

git revision
trunk / bd16e6a9023dd0a74148f3436ddbdea72338993d

Default Java
Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Multi-JDK versions
/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Test Results
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/5/testReport/

Max. process+thread count
4450 (vs. ulimit of 5500)

modules
C: hadoop-hdfs-project/hadoop-hdfs U: hadoop-hdfs-project/hadoop-hdfs

Console output
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/5/console

versions
git=2.25.1 maven=3.6.3 spotbugs=4.2.2

Powered by
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:confetti_ball: +1 overall

Vote
Subsystem
Runtime
Logfile
Comment

+0 :ok:
reexec
0m 54s

Docker mode activated.

_ Prechecks _

+1 :green_heart:
dupname
0m  0s

No case conflicting files found.

+0 :ok:
codespell
0m  0s

codespell was not available.

+0 :ok:
detsecrets
0m  0s

detect-secrets was not available.

+1 :green_heart:
@author
0m  0s

The patch does not contain any @author tags.

+1 :green_heart:
test4tests
0m  0s

The patch appears to include 1 new or modified test files.

_ trunk Compile Tests _

+1 :green_heart:
mvninstall
45m  3s

trunk passed

+1 :green_heart:
compile
1m 22s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
compile
1m 16s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
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1m 12s

trunk passed

+1 :green_heart:
mvnsite
1m 23s

trunk passed

+1 :green_heart:
javadoc
1m  7s

trunk passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m 42s

trunk passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
3m 13s

trunk passed

+1 :green_heart:
shadedclient
35m 40s

branch has no errors when building and testing our client artifacts.

_ Patch Compile Tests _

+1 :green_heart:
mvninstall
1m 10s

the patch passed

+1 :green_heart:
compile
1m 13s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javac
1m 13s

the patch passed

+1 :green_heart:
compile
1m  7s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
javac
1m  7s

the patch passed

+1 :green_heart:
blanks
0m  0s

The patch has no blanks issues.

+1 :green_heart:
checkstyle
0m 57s

the patch passed

+1 :green_heart:
mvnsite
1m 14s

the patch passed

+1 :green_heart:
javadoc
0m 51s

the patch passed with JDK Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1

+1 :green_heart:
javadoc
1m 35s

the patch passed with JDK Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

+1 :green_heart:
spotbugs
3m 17s

the patch passed

+1 :green_heart:
shadedclient
35m 55s

patch has no errors when building and testing our client artifacts.

_ Other Tests _

+1 :green_heart:
unit
278m 11s

hadoop-hdfs in the patch passed.

+1 :green_heart:
asflicense
0m 44s

The patch does not generate ASF License warnings.

420m 18s

Subsystem
Report/Notes

Docker
ClientAPI=1.45 ServerAPI=1.45 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/3/artifact/out/Dockerfile

GITHUB PR
https://github.com/apache/hadoop/pull/6694

Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell detsecrets

uname
Linux fc139e1dfaa2 5.15.0-94-generic #104-Ubuntu SMP Tue Jan 9 15:25:40 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

Build tool
maven

Personality
dev-support/bin/hadoop.sh

git revision
trunk / 47bfef529f5f69a1ae5d0f2b430df35648c47deb

Default Java
Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Multi-JDK versions
/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.22+7-post-Ubuntu-0ubuntu220.04.1 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_402-8u402-ga-2ubuntu1~20.04-b06

Test Results
https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-6694/3/testReport/

Max. process+thread count
3366 (vs. ulimit of 5500)

modules
C: hadoop-hdfs-project/hadoop-hdfs U: hadoop-hdfs-project/hadoop-hdfs

Console output
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Missing build_block smiles in results from the step of 'Generate molecules with SyntheMol'

Dear developer,
We are getting the molecule results from synthemol in the step of molecule generation. However, we noticed that some high-score molecules have missing information for the building blocks used in molecule generation.
For instance, we see the following molecule examples:
Smiles,         score,    building_block_1_1_id,    building_block_1_1_smiles,     building_block_1_2_id,    building_block_1_2_smiles
XXXXXXX,      0.98,           3000000             ,        XXXXXXXXXX               ,                  -1                      ,      NaN
Could you please help explain what does -1 and missing smile mean for  the columns  building_block_1_2_id and    building_block_1_2_smiles?
Thank you very much

Hi @JieHou-SLU,
Thank you for bringing up this issue! The -1 means that the building block SMILES was not found in the mapping from SMILES to IDs (see here). This usually should not happen when generating molecules with a single reaction as all the building blocks should appear in that mapping, so it seems like something is going wrong. I've only seen this happen when I've made a mistake providing the building blocks and reaction to building blocks mapping to SyntheMol.
Can you provide a bit more context on your generation run? Would you be able to provide the specific synthemol command that you ran? And to check, are you using the Enamine REAL building blocks and reactions from the repo or are you using any custom building blocks or reactions?
Thanks,
Kyle

Thank you for the reply. I used the following command for molecule generation:
Compute model scores for building blocks
python SyntheMol/scripts/models/predict.py
--data_path paper_data/Data/4_real_space/building_blocks.csv
--save_path experiments/models/antibiotic_chemprop/building_blocks.csv
--model_path experiments/models/antibiotic_chemprop
--model_type chemprop
--average_preds
Generate molecules
synthemol
--model_path experiments/models/antibiotic_chemprop
--model_type chemprop
--building_blocks_path experiments/models/antibiotic_chemprop/building_blocks.csv
--building_blocks_score_column chemprop_ensemble_preds
--building_blocks_id_column Reagent_ID
--reaction_to_building_blocks_path paper_data/Data/4_real_space/reaction_to_building_blocks_filtered.pkl
--save_dir experiments/models/generations_chemprop
--max_reactions 1
--n_rollout 20000
--replicate
We actually see many generated molecules have missing id/smiles for building blocks.
Thank you for your advice,

Hi Kyle，
We were trying to investigate the building blocks to address the issue, we found several questions in this process, as detailed below:

Based on the provided 'paper_data/Data/4_real_space/building_blocks.csv', there are 138060 building block smiles, with 132479 unique smiles (which matches the number in paper).
However, when we get the unique smiles from 'Data/4_real_space/reaction_to_building_blocks_filtered.pkl' (based on the command example provided on github), there are only 91429 unique smiles.

We are wondering if this is the reason why the generated molecules has missing id for the used building blocks in final results?
If this is the reason, should we choose different files for building_blocks_path and reaction_to_building_blocks_path?
synthemol
--model_path data/Models/antibiotic_chemprop
--model_type chemprop
--building_blocks_path data/Models/antibiotic_chemprop/building_blocks.csv
--building_blocks_score_column chemprop_ensemble_preds
--building_blocks_id_column Reagent_ID
--reaction_to_building_blocks_path data/Data/4_real_space/reaction_to_building_blocks_filtered.pkl
--save_dir data/Data/6_generations_chemprop
--max_reactions 1
--n_rollout 20000
--replicate
Thank you for your help,

Hi @JieHou-SLU,
Thank you for providing the additional information and apologies for the slow response!
You are correct to note that the number of unique building block SMILES in the reaction to building blocks mapping is less than the number in the building blocks file. This is because the building blocks file contains all possible building blocks, while the mapping file has been filtered to only those building blocks that are relevant to the 13 Enamine REAL reactions that we are currently using. In an upcoming new version of SyntheMol (perhaps in the next couple of months), we will introduce additional Enamine REAL reactions that will make use of more of those building blocks.
In terms of the missing SMILES issue, I did some debugging and realized that your intuition is right and there's a problem with the reaction_to_building_blocks_path file. When we originally did this work, we used one set of building blocks that lacked stereochemistry information, and then we later got an updated set of building blocks with stereochemistry. The version of building blocks in the Zenodo data is the old version without stereochemistry, so the reaction to building block mapping should have also been the non-stereochemistry version. However, I accidentally put in the new mapping instead of the old mapping.
In general, I would recommend using the new versions of the building blocks and the mapping for any projects you might be working on, and those new versions are built into SyntheMol here and are the defaults. However, if you want to specifically reproduce our work from our paper, then you'll need to use the old version of the mapping. I don't seem to have the option to upload a pickle file here, but you can recreate the old mapping with the following command.
python SyntheMol/scripts/data/filter_real_reactions_to_building_blocks.py \
    --reaction_to_building_blocks_path data/Data/4_real_space/reaction_to_building_blocks.pkl \
    --save_path data/Data/4_real_space/reaction_to_building_blocks_filtered_reproduce.pkl \
    --building_blocks_path data/Data/4_real_space/building_blocks.csv \
    --building_blocks_id_column Reagent_ID \
    --building_blocks_smiles_column smiles

Then, use this mapping in place of the one from the Zenodo data when running SyntheMol. This should also make SyntheMol faster since there won't be any missing building block SMILES during generation and so SyntheMol can make full use of the pre-computed building block scores.
Please let me know if this works for you! If so, then I'll upload the updated file to Zenodo for future users.
Best,
Kyle

Thank you very much for the detailed explanation. Yes, we have made some experiments by aligning the building blocks with reaction database, and it fully resolved the issues. Now all of generated molecules have complete ids.
Thank you for your kind support. Really appreciate it.

Okay great, I'm glad that fixed the issue!

Hi @swansonk14 , Sorry for another request for support.
We have successfully downloaded the latest Real Space database by following commands provided on real.doc with support from Enamine staff. However, we get errors when processing the *.cxsmiles.bz2 files. We also would like to build customized enamine database.
Based on the script (scripts/data/map_real_reactions_to_building_blocks.py), *.cxsmiles.bz2 files should contain the following information for reaction and reagent used in Real space molecules:
['reaction', 'reagent1', 'reagent2', 'reagent3', 'reagent4']
However, the files we downloaded from Enamine contain the following columns:
['smiles', 'id', 'MW', 'HAC', 'sLogP', 'HBA', 'HBD', 'RotBonds', 'FSP3',
'TPSA', 'Type', 'InChIKey']
I am wondering if we downloaded incorrect database?  Could you please help advise this issue?
Thank you very much,
Best,
Jie

Hi @JieHou-SLU,
I think you've likely downloaded the correct database but perhaps a different version of it. We used the 2022 q1-2 version of the Enamine REAL space that we downloaded on August 30, 2022. However, I think they have changed the format of their newer releases, so now you can only see the SMILES and associated property information but not the reagents and reactions. Unfortunately, that means that some of our scripts for processing the REAL space may no longer work. You could try asking Enamine if they can provide this older version of the REAL space, but it's possible they no longer plan to release the reagents and reactions. Even so, you should still be able to use the reagents and reactions provided as part of SyntheMol. They might not match the very latest version of the REAL space, but they should still cover about 30 billion REAL molecules.
Best,
Kyle


Canvases without associated Image Service, but only an Identifier are not recognized

This PDF is generated but pages are all empty. Loads without problems in Mirador:
https://projectmirador.org/embed/?iiif-content=https://icat.digitaldogsbody.net/iiif/1/manifest
Manifest: https://icat.digitaldogsbody.net/iiif/1/manifest
Problematic Canvas Example:
{
"id": "https://icat.digitaldogsbody.net/iiif/1/canvas/11",
"type": "Canvas",
"height": 1471,
"width": 1000,
"items": [
	{
		"id": "https://icat.digitaldogsbody.net/iiif/1/canvas/11/page",
		"type": "AnnotationPage",
		"items": [
			{
				"id": "https://icat.digitaldogsbody.net/iiif/1/canvas/11/page/image",
				"type": "Annotation",
				"motivation": "painting",
				"body": {
					"id": "https://files.transkribus.eu/Get?id=CUWUBAJLTWELOXAXSQTGJMMM&fileType=view",
					"type": "Image",
					"height": 1471,
					"width": 1000,
					"format": "image/jpg"
				},
				"target": "https://icat.digitaldogsbody.net/iiif/1/canvas/11"
			}
		]
	}
  ]
}

Originally posted by @ch-sander in https://github.com/jbaiter/pdiiif/issues/23#issuecomment-1580866890

The cause is actually a mistake in the Manifest: It uses the illegal image/jpg MIME type for the JPEG image on the Canvas annotations. The MIME type for JPEG is image/jpeg with an e, and this is what the code checks against.
@ch-sander are you in control of the icat.digitaldogsbody.net IIIF server?

Mike Bennett is. I will share this with him. Thanks for pointing out that issue.

Thanks Johannes - now fixed!

Should be fixed now


Fixed two links that were not links

What is this PR About?
$subject
How do we test this?
Click the links.
cc: @redhat-cop/rego-policies

Merged into: https://github.com/redhat-cop/rego-policies/pull/82


When tokenizing a malformed card number an api level error is raised

When tokenizing by direct post, if a card number is too short or too long Vantiv responds with an XML parse error. This is unexpected because when a card number is the appropriate length but invalid, Vantiv responds differently.
Example response with a short or long credit card number:
{
  "litleOnlineResponse": {
    "@version": "10.3",
    "@response": "1",
    "@message": "Error validating xml data against the schema on line 1\nthe length of the value is 5, but the required minimum is 13."
  },
  "RequestID": "bla"
}

Example response with an invalid card number having the appropriate length:
{
  "litleOnlineResponse": {
    "@version": "10.2",
    "@response": "0",
    "@message": "Valid Format",
    "registerTokenResponse": {
      "@id": "bla",
      "@reportGroup": "1",
      "response": "820",
      "responseTime": "2016-06-01T20:06:18",
      "message": "Credit card number was invalid",
      "TransactionID": "foo"
    }
  },
  "RequestID": "bar"
}

Also, the response (TokenizationResponse) defines a method invalid_card_number? which returns false for cards that are malformed which can be misleading.
What do we want to do for this case?

I have two thoughts so far:

I think partially this is a DevHub responsibility, to parse and standardize its responses. However, I think they think it's a API client responsibility, as they probably specify in their documentation that requests must follow certain request body format rules. I'm certain there is one in their saying that the credit card number field must be 13 characters or longer.
Given that, maybe it's a gem user responsibility. We make it a rule that the gem user needs to validate card number lengths before submission.

Still, I guess the argument could be made that it's a gem responsibility. I suppose you could change the gem to validate the field length before sending an API request to Vantiv, and have something like a PreFlightResponse that follows the LiveTransactionResponse and TiedTransactionResponse duck type, and responds to credit_card_number_invalid?.
That said, maybe it is worth it to see what happens in the eProtect iframe when you put a credit card number that is too short. Could be a way to see what their real opinion on this matter is. IE: does the eProtect form validate field length before making a request to Litle? If so, then i think for consistency, it should be the gem user's responsibility to validate that. If it does not, and it makes a request to Litle, and they handle a too-short card number in one endpoint, then maybe there is a case to be made to the Vantiv folks to also allow too-short card numbers on the direct tokenization endpoints.
Thoughts?

Closing this because we have migrated to Vantiv's XML API and this no longer applies.


Viz tests

I don't know why this pr tries to merge your commits to your own branch 0_o.
Anyway here's a flexible api chart stuff with only one TODO (expectation select's value is equal to) and Array Property -> Map String (Maybe String) conversion. I hope this code is idiomatic enough.

Hm, I'll rebase and make another pr.


Display NOC Recommendations Warning during --check phase & in Security Advisor

I'm glad we finally got the /var/cpanel/elevate-noc-recommendations file implemented in the released version. Thank you very much for pushing that through.  We are already working to apply our recommendations file to the appropriate servers on our network.
However, our testing has indicated the message is only displayed when running the --start phase of an upgrade.
This makes sense for the Accept (Y/N) functionality needing to be confirmed before processing. However, We would like our recommendation message to be displayed during the --check phase as well as the --start phase,  since that is when the user is actively troubleshooting potential blockers and is less apt to ignore the message.
We hope this will also allow for the message to be displayed as part of the Security Advisor elevate --check as well.  This could be achieved by wrapping the message in

 tags to preserve formatting when displayed on the Security Advisor page.  The hope here is to reduce the amount of users from attempting the upgrade portion sooner. Elevate Security Advisor messages are one of the ways users find out about the project so earlier display of our recommendations message is preferred to reduce overall confusion from customers.
Related to #198

Thanks Sloane,
I am familiar with the elevate-blockers and
elevate-blockers.security-advisor JSON files and experimentation with
immutable state to force the message to show up in the Security Advisor
page as an informational warning worked as expected.Accomplishing this
behavior without such a heavy handed approach as immutable state files
would definitely be the ideal solution.
So it makes sense to add an exists check that dumps the contents of the
elevate-noc-recommendations file into these JSON files proper during the
--check subroutines makes the most sense to me logistically and would
simultaneously resolve both aspects of this Ask.
The only caveat that I encountered with adding the contents of
elevate-noc-recommendations into the elevate-blockers.security-advisor
JSON files was that html tags were necessary to correct display issues with
the raw message. So we would need to at-minimum reconcile line endings with

 to properly display the notice on the security advisor page.

 tags would also probably work to satisfy formatting problems
as well.
This does beg the question if it would be preferential to use a separate
elevate-noc-recommendations.security-advisor file specifically for
passing an HTML formatted message to the Security Advisor page instead of
attempting to reconcile formatting issues. This would allow for more
elegant branded messages to appear in WHM
Thanks again for your time, effort, and consideration of my requests.
On Tue, Mar 21, 2023 at 4:00 PM Sloane Bernstein @.***>
wrote:

If we do implement this:
The assessor used in the Security Advisor gets its information by reading
a JSON blob describing the blockers, since parsing the output of the
command is far too inconsistent. We can extend the data structure to pass
along non-blocker info, as well as modify the relevant Security Advisor
assessor to look for this extra info and display it as a separate message.
I'm inclined to set the baseline severity of that new message as a warning,
though I may also clamp it so that it isn't more severe than the outcome of
the main blocker check, which even in 110 is still an informational message.
As for the message in --check, I'll have to look at what I did two weeks
ago and see if it makes sense to move things around some more to get a
non-interactive display of the message there but an interactive one for
--start.
—
Reply to this email directly, view it on GitHub
https://github.com/cpanel/elevate/issues/210#issuecomment-1478505476,
or unsubscribe
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.
You are receiving this because you authored the thread.Message ID:
@.***>

@toddr There were two parts to this ask

Primary Ask: Display contents of elevate-noc-recommendations during --check routines
Additional: Display contents of elevate-noc-recommendations in cPanel Security Advisor Page.

[ ]  Ask 1 is the main concern here. We feel it makes sense to display the contents of the file during --check  informationally since this is when an admin would be actively troubleshooting any blockers. They should be made aware of the recommendations prior to having to officially accepting them during the --start phase.

[x] Ask 2 is satisfied by the described pending change to cPanel and is a great solution for which I am grateful.

We believe Ask 1 is reasonable and very low-lift request. If preferred, I could probably put together a pull request that satisfiers this ask, but since its such a low-lift ask, figured you guys would know the best place to put it into the project where as I would splice it in willy-nilly.
Ask 2 was added as a related Ask and would have been satisfied by Ask 1 so they were included together.
Thank you for your time and consideration and I hope we can also satisfy Ask 1 too.

We already block on ask 1, so this has been met.


Failed to load resource: app/app.module

Hello, i am getting the subject error, while loading the index.html page from IISExpress, referring to the quick master project downloaded from this website. Appreciate your inputs.
" Error loading http://localhost:7041/src/app/app.module as "./app/app.module" from http://localhost:7041/src/main.js "
I am following the same directory structure. i.e src-> app-> app.module.ts and other ts files.
main.js is available under src.

This repository is now deprecated. The Angular Quickstart project was a nice starting point for creating Angular applications. Now we recommend using the Angular CLI to create new Angular projects.
Starting from 1 November 2017, all the Angular documentation, at angular.io, is based on the Angular CLI.
Let's get started


PDF Internal document links always popup security warning

Hi,
Thanks for an awesome plugin. but whenever I try and use an internal document link such as:
Background
Background
the PDF version  (When using Adobe Reader) gives me a security warning asking me whether I would like to allow this. No matter whether I click Allow or Block, it will always ask me the same question over again and the link does not work.
Any chance you could resolve this?
Thanks again!

Would be very interested in this feature, as well.

This should be fixed in v2.
Demo: links.pdf

Hello, sorry, but I will no longer maintain the project.
This project is archived because the owner no longer uses the Atom Editor.
It would be very good to find a new owner for this project, who will take care of updating and expanding the Atom package. A new version based on Chrome Headless has already been prepared in a feature branch.


Instructions for building the AIO op using libaio from conda

@tjruwase, I discovered that conda has the binary libaio package https://anaconda.org/anaconda/libaio/files, which dramatically simplifies the support for various linux distros and their versions of libaio-dev naming. Though we can't put it in requirements.txt since pypi doesn't have it and of course the user needs to use conda for the python env management, so it can't be the only option, but it's a good one where users have no perms to install packages system-wide.
If you already have libaio installed system wide, first remove it for the sake of this experiment:
# optional to test this scenario
sudo apt remove libaio-dev

Here is how to install the conda's libaio and pre-build deepspeed with it:
# activate your conda env if need be, which sets CONDA_PREFIX env var.
conda activate your-env-name

# install libaio
conda install libaio

# pre-build deepspeed
CFLAGS="-I$CONDA_PREFIX/include/" LDFLAGS="-L$CONDA_PREFIX/lib/" \
DS_BUILD_CPU_ADAM=1 DS_BUILD_AIO=1  DS_BUILD_UTILS=1 \
pip install -e . --global-option="build_ext" --global-option="-j8" \
--no-cache -v --disable-pip-version-check

Perhaps we could add this to the docs as an alternative to sudo apt install libaio-dev and if we do, I wonder if we can automate this during the pre-build, i.e. try to detect if CONDA_PREFIX env var is set and if $CONDA_PREFIX/include/" and "$CONDA_PREFIX/lib/" exist to automatically preset CFLAGS and LDFLAGS so that the user doesn't have to, unless of course they are already pre-set.

Ty but not work
(myenv) C:\Users>conda install libaio
Channels:

defaults
pytorch
Platform: win-64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

libaio

Current channels:

defaults
https://conda.anaconda.org/pytorch/win-64
https://conda.anaconda.org/pytorch/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org

and use the search bar at the top of the page.


slayerplugin: fix current task regex and new task via npc contact regex

When getting assigned a new task through NPC contact, there is no space between the word 'kill' and the killcount, thus failing the regex check.
When asking about your current assignment from a slayer master, the dialog will use a semicolon instead of a comma.
Fixes #1150

It would be best to expand the test for this.

Test class has been updated to test for the widget text regex.


Update netlify.mdx

Description (required)
related https://github.com/withastro/adapters/pull/120

Related issues & labels (optional)

Closes #
Suggested label:

Hello! Thank you for opening your first PR to Astro’s Docs! 🎉
Here’s what will happen next:

Our GitHub bots will run to check your changes.
If they spot any broken links you will see some error messages on this PR.
Don’t hesitate to ask any questions if you’re not sure what these mean!

In a few minutes, you’ll be able to see a preview of your changes on Netlify 🥳

One or more of our maintainers will take a look and may ask you to make changes.
We try to be responsive, but don’t worry if this takes a few days.

cc @Skn0tt


Adding a 'between' scope to Version

The 'following' scope is only partially useful to us; we also need to know if a change existed during a given period of time. Hence this scope.
I wanted to add tests, but I wasn't sure where you wanted them, since I didn't see a test for 'following'; if you need a test before accepting this, just let me know where to put it.

Many thanks for this, and sorry for the delay in getting back to you.
It would be great if you were able to add a test.  The following scope is implicitly exercised in the tests for version_at; that might be a good place to add a test for between.  See here.

Thanks for the pointer; I'll add a test shortly.

Updated Eric's commit with test coverage and adding a versions_between instance method on Versions.


Remove config file if user not chooses the player while setup

Closes: #36
Are you creating this PR under Hacktoberfest
Yes, I'm opening this PR under hacktoberfest.
Describe the changes you've made
I have removed the config file if user not chooses the player while setup. This solves creating a config file with empty player if users quit without choosing a player while setup yast.
Checklist:

[x] My code follows the style guidelines of this project.
[x] I have performed a self-review of my own code.
[x] I have commented my code, particularly in hard-to-understand areas.

Screenshots
Put any screenshot(s) of the project here.

Hey @murugesanp , I will review this later today. Lets close this asap.


Pagination: focus not removed after click

Steps
Click on any pagination number in docs. Item is bordered with blue (focused).
Expected Result
It should not be focused after click.
Version
0.79.0

It should be focused, it's one of accessibility ideas. See also Bootstrap docs.


Problem with onPress event

How can I handle onPress event when clicking on Tabs?
<ScrollableTabView
      style={{marginTop: 20, }}
      initialPage={0}
      renderTabBar={() => <ScrollableTabBar />}
    >
      <ListView tabLabel='Tab #1' onPress={()={this.function()}}>My Tab</ListView>

    </ScrollableTabView>;

Thank you before hand

Please describe what exactly do you want

I've got an Array with objects inside. These objects have props of id and name. So I want to make scrollable tabs with tabLabel of each with my object name props.
How can I bind onPress event with each tabLabel to do some manipulation with content inside it?

you can try onChangeTab property.

Reopen if it is not solved.


React router changes

-Originally the login page would display first when loading up the page, this changes that by removing the secure route from the landing page route in order to display the landing page first.

The change for the react router and header is to have the landing page render instead of the login.


stream-metadata: opensea refresh all member nft

should close TOWNS-12029
example: member nft

We gonna do this on-chain.


Input

Added instructions for user input values

Fixed the deleted "if" statement at the end of the file. Changed some styling stuff. Added minor functionality to incorporate the get_inputs function to the overall program.


Clarify message for unsupported QR code

See: https://github.com/threefoldtech/threefold_connect/issues/488

Re-opened
I get the error on a correct QR-scan.

This QR scans on prod with no issue, gives error on staging.


Unable to show the results with custom soulmate instance

Hi,
I have been trying to get solumate.js working in my application and in the demo page. I am using solumate as a rack mount in a rails application. Solumate seems to be sending the json right but solumate.js is not able to show the results.
The results from the server is available here. And headers from the server is available here
I tried in both the the demo page by changing the url and in my application and the result seems to be consistent.
I don't see any error in the browser console before sending a request or after the server responds. I have tested in firefox, chrome and safari.
Any help would be appreciated.
Thanks,
Ajay Kumar

Hi Ajay,
Thanks for being the first other than me to try this plugin out! I'll try to check this issue out today.
Cheers,
Mitch

In the meantime, could you let me know if the specs pass for you by opening spec/spec_runner.html in your browser?

Looks like no issues with the specs. I see 76 specs, 0 failures in 0.086sFinished at Wed Dec 21 2011 09:33:08 GMT-0800 (PST)
Let me know if you want me to tunnel my localhost to a public url so that you can see it in browser.

Strange. The response and headers look about how I would expect them to, and simulating that response on my end, I wasn't able to re-create the problem unfortunately.
Definitely, if I could access your soulmate through a public url that would be a huge help. Feel free to shoot a url to my email at<EMAIL_ADDRESS>, and I'll be able to look into it further.
Which version of soulmate are you using?
Does the demo work for you with other soulmate backends? I'm sure the seatgeek guys wouldn't mind if you fire a couple test requests to their autocomplete system, using url => 'http://seatgeek.com/autocomplete', types => ['event'] . Let me know if that works.
In case you want to get your hands a little dirty you could likely narrow the issue down by throwing a few log statements to see that requests are being made, and that the success callback is being called. Try adding a console.log line above lines 267 and 277 in jquery.soulmate.js and see what you find.


@PaperPlaneSoftware Thanks for the report! I do acknowledge this to be a bug, but I am also not sure how much we should keep supporting the idea of 2.6.+, which honestly took me a bit to remember what it means.
This is Ivyism to mean the latest sub-revision for the segment, which we used to see sometimes, but haven't seen lately since increasingly more things are published to Maven style repository. Generally I'm not a huge fan of dynamic versions since the build becomes dependent on the state of the Internet, which sbt generally tries to avoid. Also I'd be curious how +s are interpreted by Coursier.

Im having the kind of problem but with version notation like "[2,3)"
sbt thinks [2,3) is incompatible with 2.6.1 which seems incorrect to me
[error] 	* org.typelevel:cats-kernel_2.12:2.6.1 (early-semver) is selected over {[2,3), 2.0.0}
[error] 	    +- org.typelevel:cats-core_2.12:2.6.1                 (depends on 2.6.1)
[error] 	    +- ru.tcsbank.allure:base_2.12:0.2.0                  (depends on 2.0.0)
[error] 	    +- com.lucidchart:xtract_2.12:2.2.1                   (depends on [2,3))


Maintenance: migrate multiple linter tools to Ruff

As of now, we use multiple flake8 plugins along with tools like isort etc.
We can migrate to Ruff where all of these are already built-in, reducing our dependency surface and speeding up linting process by at least 10x.

Done by Ran already


Distribute releases as unlocked and/or (preferred) managed packages

Nice framework! One thing I'd like is to distribute releases as a package, rather than code. Other good open source frameworks like NebulaLogger does this, and in many projects it's the prefered way to use open source. The only other way is to adopt the source in various forms, and that always leads to modifications not contributed to the public.
By having a package changes are minimized and package versions controlled.

As discussed on LinkedIn, feel free to create this is a namespaced org and add the package details to the repo.


Unhelpful error about type parameter viewpoint

interface A[T]

actor Main
  new create(env: Env) => None

  fun a[T](xs: ReadSeq[T]): A[T] ? =>
    // works if replaced with
    // let err: box->T = xs(0)?
    let x = xs(0)?
    object
      fun apply(): box->T => x
    end

Compile error:
theodus@linux-i1mh ~/src/theodus/stuff/issue $ ponyc --version
0.16.1-dbd777a7 [release]
compiled with: llvm 3.9.1 -- clang version 3.9.1 (tags/RELEASE_391/final 289600)
theodus@linux-i1mh ~/src/theodus/stuff/issue $ ponyc -d
Building builtin -> /usr/local/lib/pony/0.16.1-dbd777a7/packages/builtin
Building . -> /home/theodus/src/theodus/stuff/issue
Error:
/home/theodus/src/theodus/stuff/issue/main.pony:7:14: only 'this', refcaps, and type parameters can be viewpoints
  fun a[T](xs: ReadSeq[T]): A[T] ? =>
             ^
Error:
/home/theodus/src/theodus/stuff/issue/main.pony:7:14: only 'this', refcaps, and type parameters can be viewpoints
  fun a[T](xs: ReadSeq[T]): A[T] ? =>
             ^

Definitely seems like pointing at the definition of xs is a problem. Talking with @jemc on the sync, it feels like this is an issue with the way x is being captured as a field in the object literal.

This is now:
Error:
/Users/sean/code/pony-scratch/issue-2132/a.pony:6:16: only 'this', refcaps, and type parameters can be viewpoints
  fun a[T](xs: ReadSeq[T]): A[T] ? =>
               ^
Error:
/Users/sean/code/pony-scratch/issue-2132/a.pony:6:16: only 'this', refcaps, and type parameters can be viewpoints
  fun a[T](xs: ReadSeq[T]): A[T] ? =>

@Theodus I believe that is what we want, yes?


Update “lit-html” dependency.

We resolved to not merge this yet. We will wait until we get the official™ 2.0 release to make this update. I'll leave the PR open to keep the context in one thread though 👍

Up to 2.0.0-rc.2 — I'll continue to keep an eye out for the first 2.0.0 release.

@klebba — Ooook. Now I think we're ready. Any reservations/hesitations? This just targets lit-html — I plan to update other things (like in dev dependencies) in a separate change set, e.g., updating eslint/puppeteer/etc.

@klebba — Update to the latest version of lit (again), lemme know if you're ok with the change?
Also, the update to puppeteer was related to an issue I hit yarn installing that super old version. Just bumping to the latest worked (and tests pass).


Trying to implement page transitions in Vue example

Hello,
It seems like the router setup for the Vue example may be preventing the transitions that are built into Vue router from properly running.  Specifically I am having issues with the leave animation.  It seems like it either gets skips or the enter state runs too quickly.  This is the code I added to AppRoot.vue
<template>

    <context-view :visible="contextViewVisible" />

    <transition name="slide-fade">
      <router-view v-if="!languageIsChanging" />
    </transition>

Language is changing...

</template>

As well as the CSS for the transition animations:
  .slide-fade-enter-active {
  transition: all 0.5s ease;
  transition-delay: 2s;
  }
  .slide-fade-leave-active {
    transition: all 1s cubic-bezier(1, 0.5, 0.8, 1);
  }
  .slide-fade-enter, .slide-fade-leave-to
  /* .slide-fade-leave-active below version 2.1.8 */ {
    transform: translateX(30px);
    opacity: 0;
  }

My guess is that it has something to do with how the dynamic routes are being fetched and the logic in  RouteHandler.vue.  I'm wondering if there are any other more simple examples of route handling that only deal with fetching the right components and mounting them with the data from SiteCore (no language switcher and graphQL stuff).
Any help is appreciated!

Response provided here: https://sitecore.stackexchange.com/questions/13993/jss-vue-page-transitions-not-fully-working-in-example-project


Nuki door sensor response time

Goodnight,
I have the Nuki 3.0 Pro connected via wifi and using your web api integration.
I have the Nuki door sensor.
My problem is the following:
When I open the door, Home Assistant takes about 28 seconds on average to receive the opening of the sensor.
This is a problem since I have made an automation so that it turns on the lights when the door is opened.
Is there an option to reduce the communication time?

Hey,

I have the Nuki 3.0 Pro connected via wifi and using your web api integration.
So you don't have any bridge, right? In this case, the integration is polling the device state using Web API (using the polling timeout you've set in configuration) and no immediate state is being pushed to the HA. That's expected.

I would expect the integration to not wait for the interval and refresh it's state immediately after issuing an action by web api.
It knows exactly that the local state is outdated at this point.
Maybe it would also be nice to expose a HA service to trigger an immediate update

I would expect the integration to not wait for the interval

I get your point, but it won't change the whole state of things much. Even if this forced refresh could detect the latest state, then it won't be updated until the next scheduled refresh, so door sensor will be reported as "open" when it's closed already.

refresh it's state immediately after issuing an action by web api

Why can't you then trigger your automation right after this?
Many, including me, just use more reliable door sensor, z-wave or zigbee for such automations and don't rely on Nuki.

Many, including me, just use more reliable door sensor, z-wave or zigbee for such automations and don't rely on Nuki.

because the sensor is already there and we do not want to use another sensor on top


Lack of draw call batching

in your kek3d/main.cpp at line 260 do not call drawarrays several times.
`for (glm::vec3 cubePosition : cubePositions)
{
glm::mat4 model = glm::mat4(1.0f);
//model = glm::translate(model, cubePosition);
//model = glm::rotate(model, glm::radians(45.0f) * (float)glfwGetTime(), glm::vec3(0.0f, 1.0f, 0.0f));
        shader.setUniformMat4(model, "model");

        glDrawArrays(GL_TRIANGLES, 0, 36);
    }`

do something like this instead, combine vertex data and pass it in one call:
`[Test]
public void GetAllVertices_Offset_Test()
{
//offset 5 blocks to the right, 1 up, 1 in.
var result = BlockMesh.GetAllVertices(new Vector3(5, 1, 1));
        Assert.AreEqual(new Vector3[]
        {
            new Vector3(4.5f, 0.5f,  0.5f), //Left Bottom Back
            new Vector3(5.5f, 0.5f,  0.5f), //Right Bottom Back
            new Vector3(5.5f, 1.5f,  0.5f), //Right Top Back
            new Vector3(4.5f, 1.5f,  0.5f), //Left Top Back - One face is completed!
            new Vector3(4.5f, 0.5f,  1.5f), //Left Bottom Front
            new Vector3(5.5f, 0.5f,  1.5f), //Right Bottom Front
            new Vector3(5.5f, 1.5f,  1.5f), //Right Top Front
            new Vector3(4.5f, 1.5f,  1.5f), //Left Top Front
        },result);
    }`

Resolved. Great comment, thanks.


Add a FAQ to the help page and improve the footer

requires the footer merge in the wazimap project

👍


any issues with forklifting out GATK and replacing with 3.8

Wondering if there is any 'secret sauce' here if I were to want to 're-wire' the GATK used by bcbio to 3.8.  Currently using bcbio-version 1.1.5a.  Wondering what config files need to be modified to downgrade.
bcbioadmin@ip-10-0-0-44> ls -l gatk4-<IP_ADDRESS>-0/
total 276473
-rwxrwxr-x 1 root root     19515 Apr  3 22:19 gatk
-rw-rw-r-- 2 root root 282832421 Mar 29 22:30 gatk-package-<IP_ADDRESS>-local.jar
bcbioadmin@ip-10-0-0-44> bcbio_nextgen.py -v
1.1.5a
bcbioadmin@ip-10-0-0-44> pwd
/mnt/fsx/share/bcbio/anaconda/share
bcbioadmin@ip-10-0-0-44>

Hi @lento2002 !
Please try this:

Install gatk3.8:
https://bcbio-nextgen.readthedocs.io/en/latest/contents/installation.html#extra-software
Use the option: tools_off: gatk4
https://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#changing-bcbio-defaults

SN

Thanks for the answer Sergey!


Phaser build using grunt throws an error

when using grunt to builkd phaser (either excluding or full build) I get the following error:
`Loading "eslint.js" tasks...ERROR

SyntaxError: C:\Work\Phaser\node_modules\grunt-eslint\tasks\eslint.js:2
const chalk = require('chalk');
^^^^^
Use of const in strict mode.`

However, the grunt process works fine, and finished without errors. Afraid to face the outcomes at a later stage :)

This should be fine since the split to Phaser CE, as I removed all the eslint files I was using :) I noticed a few left over that I've now removed too, but they weren't being used.


Ability to interrupt Python execution

Is your feature request related to a problem? Please describe.
Enter while True: pass into the Python window, and try to recover.  Ctrl-C does not work, nor does closing the Python window or pressing Clear Interpreter.  Closing the entire code browser does interrupt it, though it then pops up a number of uncaught exceptions.
Describe the solution you'd like
I should be able to use Ctrl-C or some other mechanism to either send a KeyboardInterrupt to the Python script or forcibly interrupt it..

I believe Ctrl-I interrupts, but I don't have it in front of me.  It is specified in the help.

I made the interrupt and reset actions buttons with bindable/configurable keys.  It will be in the 9.1 release.


bump version to 0.2.5

Why are these changes needed?
For new release
Related issue number

Checks

[ ] I've included any doc changes needed for https://microsoft.github.io/autogen/. See https://microsoft.github.io/autogen/docs/Contribute#documentation to build and test documentation locally.
[ ] I've added tests (if relevant) corresponding to the changes introduced in this PR.
[ ] I've made sure all auto checks have passed.

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

Comparison is base (78a2d84) 31.80% compared to head (a32cf34) 34.31%.
Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1180      +/-   ##
==========================================
+ Coverage   31.80%   34.31%   +2.50%
==========================================
  Files          29       32       +3
  Lines        4112     4301     +189
  Branches      961     1044      +83
==========================================
+ Hits         1308     1476     +168
- Misses       2710     2718       +8
- Partials       94      107      +13

Flag
Coverage Δ

unittests
34.29% <100.00%> (+2.53%)
:arrow_up:

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:loudspeaker: Have feedback on the report? Share it here.


#36 Implemented dict.keys() and dict.values() methods

Tests for dict.keys() and dict.values() methods were added (136eab043ddb3cdb36fe5a113e7c9387b312f0a7 and 36378ba4697360539da6a5c2a731c70fa1713921).

Hello!
Thanks for contributing!
I'm going to accept https://github.com/pybee/voc/pull/786 because it's more feature complete.
Thanks again!


Fix typo

a -> an

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

Verified editorial corrections.


SEO - Inspect Meta Tag

Checking the current condition of meta tag, add the basic requirements of meta tags.
Check social media share also.

Still need to add meta tag for each page I think


Lots of warnings when running test suite

While replicating #109, I noticed a lot of warnings logged from the command python3 -m pytest -v. They are a mixture of DeprecationWarnings and RemovedInPytest4Warnings.
I've pasted the output below the fold so we can track which packages need updating.
Output
/Users/sgibson/anaconda3/lib/python3.7/site-packages/matplotlib/rcsetup.py:20: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import Iterable, Mapping

/Users/sgibson/anaconda3/lib/python3.7/site-packages/matplotlib/colors.py:53: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import Sized

/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)

/Users/sgibson/scona/tests/make_corr_matrices_test.py:38: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:38: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:38: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:38: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_data" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/fixtures.py:977: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  return function(*args, **kwargs)
/Users/sgibson/scona/scona/make_corr_matrices.py:63: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

/Users/sgibson/scona/tests/make_corr_matrices_test.py:47: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:47: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:47: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:47: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  subject_array()[:, i]) for i in [0, 1]]
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_data" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/fixtures.py:977: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  return function(*args, **kwargs)
/Users/sgibson/scona/scona/make_corr_matrices.py:63: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

/Users/sgibson/scona/tests/make_corr_matrices_test.py:56: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:56: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:56: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  for i in [0, 1]]
/Users/sgibson/scona/tests/make_corr_matrices_test.py:56: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  for i in [0, 1]]
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_data" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/fixtures.py:977: RemovedInPytest4Warning: Fixture "subject_array" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  return function(*args, **kwargs)
/Users/sgibson/scona/scona/make_corr_matrices.py:63: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)
/Users/sgibson/scona/scona/make_corr_matrices.py:121: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

/Users/sgibson/anaconda3/lib/python3.7/site-packages/_pytest/python.py:197: RemovedInPytest4Warning: Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly, are created automatically when test functions request them as parameters. See https://docs.pytest.org/en/latest/fixture.html for more information.
  testfunction(**testargs)
/Users/sgibson/scona/scona/make_corr_matrices.py:121: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)
/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/anaconda3/lib/python3.7/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
  warnings.warn(msg, DeprecationWarning)

/Users/sgibson/scona/scona/make_corr_matrices.py:63: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:
/Users/sgibson/scona/scona/make_corr_matrices.py:121: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
  if non_numeric_cols:

-- Docs: https://docs.pytest.org/en/latest/warnings.html

For the record, I am using:
anaconda Command line client (version 1.7.2)
Python 3.7.0

So, mixed results to setting up an environment.
Here's what I did:
conda create --name scona python=3.6
pip install git+https://github.com/WhitakerLab/scona.git
pip install -r requirements  # had to run this otherwise pytest wasn't installed

The amount of warnings were greatly reduced!
Warnings output
  /Users/sgibson/anaconda3/envs/scona/lib/python3.6/site-packages/networkx/classes/graph.py:766: DeprecationWarning: add_path is deprecated. Use nx.add_path instead.
    warnings.warn(msg, DeprecationWarning)

tests/regression_test.py::FixturesTest::test_corrmat_matches_fixture
  /Users/sgibson/scona/scona/make_corr_matrices.py:63: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
    if non_numeric_cols:

tests/regression_test.py::FixturesTest::test_corrmat_matches_fixture
  /Users/sgibson/scona/scona/make_corr_matrices.py:121: DeprecationWarning: The truth value of an empty array is ambiguous. Returning False, but in future this will result in an error. Use `array.size > 0` to check that an array is not empty.
    if non_numeric_cols:

But now 7 tests are failing instead of 1:
Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.

test_create_residuals_df_covars_plural

Fixture "subject_array" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.

test_create_residuals_df_covars_singular

Fixture "subject_array" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
*test_create_residuals_df_covars_none
Fixture "subject_array" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.

test_create_corrmat_pearson

Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.

test_create_corrmat_spearman

Fixture "subject_residuals" called directly. Fixtures are not meant to be called directly,
but are created automatically when test functions request them as parameters.
See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.

FixturesTest.test_lm_against_fixture

self = <tests.regression_test.FixturesTest testMethod=test_lm_against_fixture>

    def test_lm_against_fixture(self):
        # test new local measures against fixture
        print('\ntesting new nodal measures against fixture')
        self.assertEqual(self.hash_dict_new[self.lm],
>                        self.hash_dict_original[self.lm])
E       AssertionError: '3ce452749b52e3a60b7779ffe3c43e1de8219cb42715aeabd28b94363b59e9bb' != 'dc585cb573b87b1099c034f7c6991c410fca3f6878541e3caa2c7ac0816957dc'
E       - 3ce452749b52e3a60b7779ffe3c43e1de8219cb42715aeabd28b94363b59e9bb
E       + dc585cb573b87b1099c034f7c6991c410fca3f6878541e3caa2c7ac0816957dc

tests/regression_test.py:37: AssertionError

Hi @sgibson91!
Have you the following test passed when you run locally?

FixturesTest.test_rich_against_fixture
FixturesTest.test_lm_against_fixture
FixturesTest.test_gm_against_fixture

FixturesTest.test_rich_against_fixture ✅
FixturesTest.test_lm_against_fixture 🚫
FixturesTest.test_gm_against_fixture ✅

I've made some changes in the pytestwarnings branch. For me all warnings have disappeared (although the failing tests still fail)

closing