[cytoscape/cytoscape-gui-distribution] 090c96: Update biopax version

2019-05-15 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 090c965cc5a9cdba6d018ab28776a7fff80d8d4e
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/090c965cc5a9cdba6d018ab28776a7fff80d8d4e
  Author: Unknown 
  Date:   2019-05-15 (Wed, 15 May 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Update biopax version


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[cytoscape/cytoscape] 7246d2: Update README.md

2019-06-06 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape
  Commit: 7246d29f69dc1bb33268dacc6d59993ee9a0469e
  
https://github.com/cytoscape/cytoscape/commit/7246d29f69dc1bb33268dacc6d59993ee9a0469e
  Author: dotasek 
  Date:   2019-06-06 (Thu, 06 Jun 2019)

  Changed paths:
M README.md

  Log Message:
  ---
  Update README.md

Add link to bug report page


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[cytoscape/cytoscape-gui-distribution] 3c8451: Update to mockito-core

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 3c84513874c2a098f21abcd90978138aec0a4438
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/3c84513874c2a098f21abcd90978138aec0a4438
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M integration-test/pom.xml

  Log Message:
  ---
  Update to mockito-core


  Commit: 749afdd246e368475e3b69e72dcf309057e662be
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/749afdd246e368475e3b69e72dcf309057e662be
  Author: D 
  Date:   2019-05-30 (Thu, 30 May 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/xsl/template.xslt

  Log Message:
  ---
  Add linux openjfx jars to assembly


  Commit: ea1a54e72101b0125de9bc0b2d6db1cf306d7c51
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/ea1a54e72101b0125de9bc0b2d6db1cf306d7c51
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Add patch modules for javax in bat and sh files


  Commit: 8d6c1ee6f0856a8cfae351216540e8eb63734d72
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/8d6c1ee6f0856a8cfae351216540e8eb63734d72
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  parameterize module names (no hardcoded karaf version)


  Commit: b996e97066057a8e4518c96178bdf3c06c8a439e
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/b996e97066057a8e4518c96178bdf3c06c8a439e
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt

  Log Message:
  ---
  Add mac dependencies and OS specific JavaFX handling


  Commit: 88ba88d453e77631146d93e6b286586c2890e1ac
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/88ba88d453e77631146d93e6b286586c2890e1ac
  Author: D 
  Date:   2019-07-12 (Fri, 12 Jul 2019)

  Changed paths:
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Switch to java.awt.Desktop


  Commit: f52a6039d63b102d1a319c4205c6cc742507f681
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/f52a6039d63b102d1a319c4205c6cc742507f681
  Author: D 
  Date:   2019-07-12 (Fri, 12 Jul 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Merge branch 'openjfx' into java11


  Commit: ca3d91b06cd171ac623325be8eacc42a71ceada6
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/ca3d91b06cd171ac623325be8eacc42a71ceada6
  Author: D 
  Date:   2019-07-16 (Tue, 16 Jul 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Merge remote-tracking branch 'dotasek/java11' into java11


Compare: 
https://github.com/cytoscape/cytoscape-gui-distribution/compare/3c84513874c2%5E...ca3d91b06cd1

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[cytoscape/cytoscape-api] b92b7b: Temporarily remove breaking javadoc compile and ta...

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: b92b7b84eef2ebac6970be71bb817fdd270ba231
  
https://github.com/cytoscape/cytoscape-api/commit/b92b7b84eef2ebac6970be71bb817fdd270ba231
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
M app-api/pom.xml
M pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Temporarily remove breaking javadoc compile and taglets


  Commit: c0f4050007c50161b92ef12adc4aff813fdb0d8f
  
https://github.com/cytoscape/cytoscape-api/commit/c0f4050007c50161b92ef12adc4aff813fdb0d8f
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
M property-api/pom.xml

  Log Message:
  ---
  Update maven-jaxb2-plugin version


  Commit: 81be9021a83e3dfe7832e29cce882b307f559442
  
https://github.com/cytoscape/cytoscape-api/commit/81be9021a83e3dfe7832e29cce882b307f559442
  Author: D 
  Date:   2019-05-22 (Wed, 22 May 2019)

  Changed paths:
M 
layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
M 
swing-util-api/src/main/java/org/cytoscape/util/swing/BasicCollapsiblePanel.java
M 
swing-util-api/src/main/java/org/cytoscape/util/swing/DropDownMenuButton.java
R swing-util-api/src/main/resources/images/arrow_collapsed.png
R swing-util-api/src/main/resources/images/arrow_expanded.png
M util-api/src/main/java/org/cytoscape/util/color/Palette.java
M work-api/src/main/java/org/cytoscape/work/util/ListChangeListener.java

  Log Message:
  ---
  Merge remote-tracking branch 'origin/develop' into java11


  Commit: 7d61838be9bb1cbb77cbf0b53587ef0d42451131
  
https://github.com/cytoscape/cytoscape-api/commit/7d61838be9bb1cbb77cbf0b53587ef0d42451131
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M api-bundle/pom.xml

  Log Message:
  ---
  Use parent bundle plugin


  Commit: 5e7a041ac58c0158b0f83660c3ea16c5b722e5bc
  
https://github.com/cytoscape/cytoscape-api/commit/5e7a041ac58c0158b0f83660c3ea16c5b722e5bc
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M property-api/pom.xml

  Log Message:
  ---
  Add jaxb dependences + update to mockito-core


  Commit: d350362979148e36ae187448f6ce57748642a9bb
  
https://github.com/cytoscape/cytoscape-api/commit/d350362979148e36ae187448f6ce57748642a9bb
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M app-api/pom.xml
M application-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M pom.xml
M presentation-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Update to mockito-core


  Commit: 5dccf45f2a038aee5e71a0e1b9d5785ee74b6fb1
  
https://github.com/cytoscape/cytoscape-api/commit/5dccf45f2a038aee5e71a0e1b9d5785ee74b6fb1
  Author: D 
  Date:   2019-05-30 (Thu, 30 May 2019)

  Changed paths:
M jobs-api/pom.xml

  Log Message:
  ---
  Fix inherited groupId


  Commit: 4a0b20ddd9f2d8739409aabeb40310e8992ff946
  
https://github.com/cytoscape/cytoscape-api/commit/4a0b20ddd9f2d8739409aabeb40310e8992ff946
  Author: D 
  Date:   2019-05-30 (Thu, 30 May 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Some attempts to  fix javadoc production


  Commit: 23e9d84164931d7afe60ba952b97af6617e2b91a
  
https://github.com/cytoscape/cytoscape-api/commit/23e9d84164931d7afe60ba952b97af6617e2b91a
  Author: Cytoscape 
  Date:   2019-05-30 (Thu, 30 May 2019)

  Changed paths:
M 
layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithmManager.java
M 
swing-util-api/src/main/java/org/cytoscape/util/swing/BasicCollapsiblePanel.java
M 
swing-util-api/src/main/java/org/cytoscape/util/swing/DropDownMenuButton.java
R swing-util-api/src/main/resources/images/arrow_collapsed.png
R swing-util-api/src/main/resources/images/arrow_expanded.png
M util-api/src/main/java/org/cytoscape/util/color/Palette.java
M work-api/src/main/java/org/cytoscape/work/util/ListChangeListener.java

  Log Message:
  ---
  Merge branch 'develop' of github.com:cytoscape/cytoscape-api into develop

Merge to Java 11 branch


  Commit: 2a67d10239ee6f7bce0a49898740354caed50a1f
  
https://github.com/cytoscape/cytoscape-api/commit/2a67d10239ee6f7bce0a49898740354caed50a1f
  Author: Cytoscape 
  Date:   2019-06-03 (Mon, 03 Jun 2019)

  Changed paths:

[cytoscape/cytoscape] 1673c7: Add java.xml bind module for Java 11 build

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape
  Commit: 1673c795d129cff330785d3593f4ab030fecd146
  
https://github.com/cytoscape/cytoscape/commit/1673c795d129cff330785d3593f4ab030fecd146
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
A .mvn/jvm.config

  Log Message:
  ---
  Add java.xml bind module for Java 11 build


  Commit: ca917f346192b2aff361aa5511271dd114378fd3
  
https://github.com/cytoscape/cytoscape/commit/ca917f346192b2aff361aa5511271dd114378fd3
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M .mvn/jvm.config

  Log Message:
  ---
  Remove add module; use mvn dependencies instead


Compare: 
https://github.com/cytoscape/cytoscape/compare/1673c795d129%5E...ca917f346192

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[cytoscape/cytoscape-parent] d2bf73: Update karaf and maven compiler version disable ja...

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: d2bf734b4ad58224fd5d46f0e16445d340d08e74
  
https://github.com/cytoscape/cytoscape-parent/commit/d2bf734b4ad58224fd5d46f0e16445d340d08e74
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update karaf and maven compiler version disable javadoc


  Commit: 108fa811e8c2ef11e452d2baa879fcb2424d36b7
  
https://github.com/cytoscape/cytoscape-parent/commit/108fa811e8c2ef11e452d2baa879fcb2424d36b7
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update maven and mockito versions


  Commit: 1bc3b0c9c08a49d09f0f6f45685b6fc9ff2643e4
  
https://github.com/cytoscape/cytoscape-parent/commit/1bc3b0c9c08a49d09f0f6f45685b6fc9ff2643e4
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update maven and java versions


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/d2bf734b4ad5%5E...1bc3b0c9c08a

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[cytoscape/cytoscape-app-template]

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-app-template

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[cytoscape/cytoscape-support]

2019-07-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-support

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[cytoscape/cytoscape] b0edd9: Call cy.sh from travis

2019-08-13 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape
  Commit: b0edd99046cd4bf9929d9ce7b3f7c94b9630c7e3
  
https://github.com/cytoscape/cytoscape/commit/b0edd99046cd4bf9929d9ce7b3f7c94b9630c7e3
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Call cy.sh from travis


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[cytoscape/cytoscape] 34ef7b: Create .travis.settings.xml

2019-08-13 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape
  Commit: 34ef7b5a73eaa43e549789c2a8f1b252c6e51435
  
https://github.com/cytoscape/cytoscape/commit/34ef7b5a73eaa43e549789c2a8f1b252c6e51435
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
A .travis.settings.xml

  Log Message:
  ---
  Create .travis.settings.xml


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[cytoscape/cytoscape] 8683c1: Create .travis.yml

2019-08-13 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape
  Commit: 8683c11d3876b0f1d1053dbc5e98b8956130d101
  
https://github.com/cytoscape/cytoscape/commit/8683c11d3876b0f1d1053dbc5e98b8956130d101
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
A .travis.yml

  Log Message:
  ---
  Create .travis.yml


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[cytoscape/cytoscape-gui-distribution] 2d0b6a: Add deploy

2019-07-29 Thread dotasek
  Branch: refs/heads/travis-ci
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 2d0b6a8431b0c5ca7626a876c1e5af3e2e7607a3
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/2d0b6a8431b0c5ca7626a876c1e5af3e2e7607a3
  Author: Unknown 
  Date:   2019-07-29 (Mon, 29 Jul 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Add deploy


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[cytoscape/cytoscape-api] 77de9f: Update .travis.yml

2019-08-02 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 77de9f3eea351f951265ce9423e715cd4de863ee
  
https://github.com/cytoscape/cytoscape-api/commit/77de9f3eea351f951265ce9423e715cd4de863ee
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-api] 76a888: Update .travis.yml

2019-08-02 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 76a8880a4daf6530f8756ec35da6f76c820d4c45
  
https://github.com/cytoscape/cytoscape-api/commit/76a8880a4daf6530f8756ec35da6f76c820d4c45
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-api] cac2b8: Change xvfb declaration

2019-08-02 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: cac2b8cb20abc448d13dcc6e81b604256be67062
  
https://github.com/cytoscape/cytoscape-api/commit/cac2b8cb20abc448d13dcc6e81b604256be67062
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Change xvfb declaration


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[cytoscape/cytoscape-api] 0f1390: Update repos to nrnb-nexus

2019-08-02 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 0f1390b6a8f336fb5f2d6c3af60e3159faf81fcc
  
https://github.com/cytoscape/cytoscape-api/commit/0f1390b6a8f336fb5f2d6c3af60e3159faf81fcc
  Author: D 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M api-bundle/pom.xml
M application-api/pom.xml
M ci-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M filter-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M presentation-api/pom.xml
M property-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M util-api/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Update repos to nrnb-nexus


  Commit: 038b60974599c2f3a9afaf794df8c577fb7d133a
  
https://github.com/cytoscape/cytoscape-api/commit/038b60974599c2f3a9afaf794df8c577fb7d133a
  Author: D 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Remove duplicate version


  Commit: bb4e8f90dac723ebcf7d1bbf9aafc30b965a5f05
  
https://github.com/cytoscape/cytoscape-api/commit/bb4e8f90dac723ebcf7d1bbf9aafc30b965a5f05
  Author: D 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
A .travis.settings.xml
M .travis.yml

  Log Message:
  ---
  Update travis.yml add travis.settings.xml


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/21fcfb003696...bb4e8f90dac7

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[cytoscape/cytoscape-api] 4b7a51: Add display and xvfb to solve travis headless exce...

2019-08-02 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 4b7a51e77390dff4971f6fddac462e0e54fd634e
  
https://github.com/cytoscape/cytoscape-api/commit/4b7a51e77390dff4971f6fddac462e0e54fd634e
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Add display and xvfb to solve travis headless exception


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[cytoscape/cytoscape-api] d2446a: taglet refactor

2019-08-14 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  
https://github.com/cytoscape/cytoscape-api/commit/d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  taglet refactor


  Commit: 210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  
https://github.com/cytoscape/cytoscape-api/commit/210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Update javadoc link sources


  Commit: 00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  
https://github.com/cytoscape/cytoscape-api/commit/00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Uncomment taglets


  Commit: ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  
https://github.com/cytoscape/cytoscape-api/commit/ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M swing-application-api/pom.xml

  Log Message:
  ---
  Add javax as dependency


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/d2446a8e5ef6%5E...ed32615bc832

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[cytoscape/cytoscape-impl] d44e09: Add javax dependencies

2019-08-14 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: d44e09ea7fed2c1f952b7073feac6726588a9913
  
https://github.com/cytoscape/cytoscape-impl/commit/d44e09ea7fed2c1f952b7073feac6726588a9913
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M pom.xml
M swing-application-impl/pom.xml

  Log Message:
  ---
  Add javax dependencies


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[cytoscape/cytoscape-gui-distribution]

2019-08-16 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-api] cdf9f9: Switch to regular jar instead of aggregate jar for...

2019-08-16 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  
https://github.com/cytoscape/cytoscape-api/commit/cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Switch to regular jar instead of aggregate jar for javadoc


  Commit: 15fec711bc28972b9e692c66430d097e95bd8f08
  
https://github.com/cytoscape/cytoscape-api/commit/15fec711bc28972b9e692c66430d097e95bd8f08
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M property-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Enable javadoc generation for swing-app-api


  Commit: 0cd2a105e3ded7534fd8d541d8178e675f38e676
  
https://github.com/cytoscape/cytoscape-api/commit/0cd2a105e3ded7534fd8d541d8178e675f38e676
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Remove explicit links from javadoc (inherit intead)


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/ed32615bc832...0cd2a105e3de

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[cytoscape/cytoscape-gui-distribution] 3c8451: Update to mockito-core

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 3c84513874c2a098f21abcd90978138aec0a4438
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/3c84513874c2a098f21abcd90978138aec0a4438
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M integration-test/pom.xml

  Log Message:
  ---
  Update to mockito-core


  Commit: 749afdd246e368475e3b69e72dcf309057e662be
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/749afdd246e368475e3b69e72dcf309057e662be
  Author: D 
  Date:   2019-05-30 (Thu, 30 May 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/xsl/template.xslt

  Log Message:
  ---
  Add linux openjfx jars to assembly


  Commit: ea1a54e72101b0125de9bc0b2d6db1cf306d7c51
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/ea1a54e72101b0125de9bc0b2d6db1cf306d7c51
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Add patch modules for javax in bat and sh files


  Commit: 8d6c1ee6f0856a8cfae351216540e8eb63734d72
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/8d6c1ee6f0856a8cfae351216540e8eb63734d72
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  parameterize module names (no hardcoded karaf version)


  Commit: b996e97066057a8e4518c96178bdf3c06c8a439e
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/b996e97066057a8e4518c96178bdf3c06c8a439e
  Author: D 
  Date:   2019-05-31 (Fri, 31 May 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt

  Log Message:
  ---
  Add mac dependencies and OS specific JavaFX handling


  Commit: 88ba88d453e77631146d93e6b286586c2890e1ac
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/88ba88d453e77631146d93e6b286586c2890e1ac
  Author: D 
  Date:   2019-07-12 (Fri, 12 Jul 2019)

  Changed paths:
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Switch to java.awt.Desktop


  Commit: f52a6039d63b102d1a319c4205c6cc742507f681
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/f52a6039d63b102d1a319c4205c6cc742507f681
  Author: D 
  Date:   2019-07-12 (Fri, 12 Jul 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Merge branch 'openjfx' into java11


  Commit: ca3d91b06cd171ac623325be8eacc42a71ceada6
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/ca3d91b06cd171ac623325be8eacc42a71ceada6
  Author: D 
  Date:   2019-07-16 (Tue, 16 Jul 2019)

  Changed paths:
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.sh
M assembly/src/main/xsl/template.xslt
M launcher/src/main/java/org/cytoscape/launcher/internal/MacHelper.java

  Log Message:
  ---
  Merge remote-tracking branch 'dotasek/java11' into java11


  Commit: e1caf234ee403e02fa2f26aea839df761d3c0676
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/e1caf234ee403e02fa2f26aea839df761d3c0676
  Author: D 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M 
integration-test/src/test/java/org/cytoscape/session/Cy252SimpleSessionLodingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy263SimpleSessionLodingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy270SimpleSessionLodingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy283ComplexSessionLodingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy283GroupsSessionLoadingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3CollapsedGroupsSessionLoadingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3ExpandedGroupsSessionLoadingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3GroupsSessionLoadingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3SimpleSessionLodingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3SubnetworksSessionLoadingTest.java
M 
integration-test/src/test/java/org/cytoscape/session/Cy3VisualMappingsSessionLoadingTest.java

  Log Message:
  ---
  Ignore failing tests


  Commit: c143734a82a72df0f88e5b62d083bc2bba9a6707
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/c143734a82a72df0f88e5b62d083bc2bba9a6707
  Author: D 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M packaging/pom.xml
M splash-updater-impl/pom.xml
M third-party/pom.xml

  Log Message:
  ---
  Update to ucsd nexus repo


  Commit

[cytoscape/cytoscape-parent] d2bf73: Update karaf and maven compiler version disable ja...

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: d2bf734b4ad58224fd5d46f0e16445d340d08e74
  
https://github.com/cytoscape/cytoscape-parent/commit/d2bf734b4ad58224fd5d46f0e16445d340d08e74
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update karaf and maven compiler version disable javadoc


  Commit: 108fa811e8c2ef11e452d2baa879fcb2424d36b7
  
https://github.com/cytoscape/cytoscape-parent/commit/108fa811e8c2ef11e452d2baa879fcb2424d36b7
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update maven and mockito versions


  Commit: 1bc3b0c9c08a49d09f0f6f45685b6fc9ff2643e4
  
https://github.com/cytoscape/cytoscape-parent/commit/1bc3b0c9c08a49d09f0f6f45685b6fc9ff2643e4
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update maven and java versions


  Commit: a993199e41c82b513d829c4c1cfb7c9c4893838b
  
https://github.com/cytoscape/cytoscape-parent/commit/a993199e41c82b513d829c4c1cfb7c9c4893838b
  Author: D 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
A .travis.settings.xml
M pom.xml

  Log Message:
  ---
  Update nexus settings for travis builds


  Commit: 1d3b0cff98002bcab3dfcacca9db9b0c57cb46f0
  
https://github.com/cytoscape/cytoscape-parent/commit/1d3b0cff98002bcab3dfcacca9db9b0c57cb46f0
  Author: D 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: f30f760a525491a423e1038e359a657089876e86
  
https://github.com/cytoscape/cytoscape-parent/commit/f30f760a525491a423e1038e359a657089876e86
  Author: D 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 7071038ff8be735e568b050465762e810a6559c7
  
https://github.com/cytoscape/cytoscape-parent/commit/7071038ff8be735e568b050465762e810a6559c7
  Author: D 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Adjust travis deploy branch


  Commit: bf0e4eaa69c634a72387e0c584afb7ff0ffa099b
  
https://github.com/cytoscape/cytoscape-parent/commit/bf0e4eaa69c634a72387e0c584afb7ff0ffa099b
  Author: D 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Set deploy on branch java11


  Commit: 44f57560b3ed29df372ddade980fb6f01a04b378
  
https://github.com/cytoscape/cytoscape-parent/commit/44f57560b3ed29df372ddade980fb6f01a04b378
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Enable javadoc plugin


  Commit: 8c60243df3a4512df2d23be83e3cc713b157e5c4
  
https://github.com/cytoscape/cytoscape-parent/commit/8c60243df3a4512df2d23be83e3cc713b157e5c4
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Merge branch 'java11-javadoc' into java11


  Commit: cd8b638f313e81ace049f25af03d7736581d0282
  
https://github.com/cytoscape/cytoscape-parent/commit/cd8b638f313e81ace049f25af03d7736581d0282
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
A .travis.settings.xml
M .travis.yml
M pom.xml

  Log Message:
  ---
  Merge branch 'java11' into develop


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/df42bdb588cd...cd8b638f313e

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[cytoscape/cytoscape-impl] 420199: Add jaxb imports for table import, fix cast errors

2019-08-19 Thread dotasek
 vizmap-gui-core-impl/pom.xml
M vizmap-impl/pom.xml
M webservice-impl/pom.xml
M work-headless-impl/pom.xml
M work-impl/pom.xml
M work-swing-impl/pom.xml

  Log Message:
  ---
  Update repository references to ucsd nexus


  Commit: 50d082760fa3b1291e2edceaaf6d15bd28d36ad0
  
https://github.com/cytoscape/cytoscape-impl/commit/50d082760fa3b1291e2edceaaf6d15bd28d36ad0
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
A .travis.settings.xml

  Log Message:
  ---
  Create .travis.settings.xml


  Commit: 49651a21691cc8f8f6aeb01ceddc221f5c5ad7c2
  
https://github.com/cytoscape/cytoscape-impl/commit/49651a21691cc8f8f6aeb01ceddc221f5c5ad7c2
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
A .travis.yml

  Log Message:
  ---
  Create .travis.yml


  Commit: e17671853ac8ecaee1d624e96867bad90e6eee2d
  
https://github.com/cytoscape/cytoscape-impl/commit/e17671853ac8ecaee1d624e96867bad90e6eee2d
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Make travis build skip initial install


  Commit: b287517b293d83a7a3ae0133d8c0dac69843c912
  
https://github.com/cytoscape/cytoscape-impl/commit/b287517b293d83a7a3ae0133d8c0dac69843c912
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 38d243bc1a6b3829e96c1cda697012fb61d8937f
  
https://github.com/cytoscape/cytoscape-impl/commit/38d243bc1a6b3829e96c1cda697012fb61d8937f
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 43d682b491431bdfd1c7dfb3928284d4275a7957
  
https://github.com/cytoscape/cytoscape-impl/commit/43d682b491431bdfd1c7dfb3928284d4275a7957
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: fb5453304637362c52bee0c2ae4f567f0045dbdb
  
https://github.com/cytoscape/cytoscape-impl/commit/fb5453304637362c52bee0c2ae4f567f0045dbdb
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 13a2234680ca7a08e7e218ab7d878469b4e7529f
  
https://github.com/cytoscape/cytoscape-impl/commit/13a2234680ca7a08e7e218ab7d878469b4e7529f
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: d232cddf873bb8a0e8691ca1398604355815755d
  
https://github.com/cytoscape/cytoscape-impl/commit/d232cddf873bb8a0e8691ca1398604355815755d
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: bb098f6bb25e7f405663840da1ce40fceddebc2e
  
https://github.com/cytoscape/cytoscape-impl/commit/bb098f6bb25e7f405663840da1ce40fceddebc2e
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: cf93d9342c67a41b1ef383d1691dd39a5aa75668
  
https://github.com/cytoscape/cytoscape-impl/commit/cf93d9342c67a41b1ef383d1691dd39a5aa75668
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 29514d32fa19a1b8c5bac9558bd59c6a84d834a7
  
https://github.com/cytoscape/cytoscape-impl/commit/29514d32fa19a1b8c5bac9558bd59c6a84d834a7
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: d44e09ea7fed2c1f952b7073feac6726588a9913
  
https://github.com/cytoscape/cytoscape-impl/commit/d44e09ea7fed2c1f952b7073feac6726588a9913
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M pom.xml
M swing-application-impl/pom.xml

  Log Message:
  ---
  Add javax dependencies


  Commit: d05678fb79b1ba8036bef23ac3e1cee4910f262c
  
https://github.com/cytoscape/cytoscape-impl/commit/d05678fb79b1ba8036bef23ac3e1cee4910f262c
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/internal/util/ViewUtil.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpReportABugTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTaskFactory.java

[cytoscape/cytoscape-api] b92b7b: Temporarily remove breaking javadoc compile and ta...

2019-08-19 Thread dotasek
 add travis.settings.xml


  Commit: 76a8880a4daf6530f8756ec35da6f76c820d4c45
  
https://github.com/cytoscape/cytoscape-api/commit/76a8880a4daf6530f8756ec35da6f76c820d4c45
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 77de9f3eea351f951265ce9423e715cd4de863ee
  
https://github.com/cytoscape/cytoscape-api/commit/77de9f3eea351f951265ce9423e715cd4de863ee
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 4b7a51e77390dff4971f6fddac462e0e54fd634e
  
https://github.com/cytoscape/cytoscape-api/commit/4b7a51e77390dff4971f6fddac462e0e54fd634e
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Add display and xvfb to solve travis headless exception


  Commit: cac2b8cb20abc448d13dcc6e81b604256be67062
  
https://github.com/cytoscape/cytoscape-api/commit/cac2b8cb20abc448d13dcc6e81b604256be67062
  Author: dotasek 
  Date:   2019-08-02 (Fri, 02 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Change xvfb declaration


  Commit: 90633763a6d6b94b355be1b25e865de01ee122fb
  
https://github.com/cytoscape/cytoscape-api/commit/90633763a6d6b94b355be1b25e865de01ee122fb
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  
https://github.com/cytoscape/cytoscape-api/commit/d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  taglet refactor


  Commit: 210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  
https://github.com/cytoscape/cytoscape-api/commit/210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Update javadoc link sources


  Commit: 00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  
https://github.com/cytoscape/cytoscape-api/commit/00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Uncomment taglets


  Commit: ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  
https://github.com/cytoscape/cytoscape-api/commit/ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M swing-application-api/pom.xml

  Log Message:
  ---
  Add javax as dependency


  Commit: cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  
https://github.com/cytoscape/cytoscape-api/commit/cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Switch to regular jar instead of aggregate jar for javadoc


  Commit: 15fec711bc28972b9e692c66430d097e95bd8f08
  
https://github.com/cytoscape/cytoscape-api/commit/15fec711bc28972b9e692c66430d097e95bd8f08
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M property-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Enable javadoc generation for swing-app-api


  Commit: 0cd2a105e3ded7534fd8d541d8178e675f38e676
  
https://github.com/cytoscape/cytoscape-api/commit/0cd2a105e3ded7534fd8d541d8178e675f38e676
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Remove explicit links from javadoc (inherit intead)


  Commit: 154ddfc297b4a5438f2324446fa8eaf635c95d89
  
https://github.com/cytoscape/cytoscape-api/commit/154ddfc297b4a5438f2324446fa8eaf635c95d89
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M app-api/pom.xml
M pom.xml
M property-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility

[cytoscape/cytoscape-app-template] f28292: Update to ucsd nexus, remove javadoc unpack.

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-app-template
  Commit: f282928ad8bdb935e16d13fadaf4096242e4cf43
  
https://github.com/cytoscape/cytoscape-app-template/commit/f282928ad8bdb935e16d13fadaf4096242e4cf43
  Author: D 
  Date:   2019-08-08 (Thu, 08 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update to ucsd nexus, remove javadoc unpack.


  Commit: 8fbcd8bebb777b140deab593e001dceb0159c96e
  
https://github.com/cytoscape/cytoscape-app-template/commit/8fbcd8bebb777b140deab593e001dceb0159c96e
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Restore unpack-javadoc, update dependency plugin


  Commit: 652de74c68c423a875113cc5217cb21a4453ed53
  
https://github.com/cytoscape/cytoscape-app-template/commit/652de74c68c423a875113cc5217cb21a4453ed53
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Merge branch 'java11' into develop


Compare: 
https://github.com/cytoscape/cytoscape-app-template/compare/6a8a69b11dad...652de74c68c4

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[cytoscape/cytoscape] 1673c7: Add java.xml bind module for Java 11 build

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape
  Commit: 1673c795d129cff330785d3593f4ab030fecd146
  
https://github.com/cytoscape/cytoscape/commit/1673c795d129cff330785d3593f4ab030fecd146
  Author: D 
  Date:   2019-03-26 (Tue, 26 Mar 2019)

  Changed paths:
A .mvn/jvm.config

  Log Message:
  ---
  Add java.xml bind module for Java 11 build


  Commit: ca917f346192b2aff361aa5511271dd114378fd3
  
https://github.com/cytoscape/cytoscape/commit/ca917f346192b2aff361aa5511271dd114378fd3
  Author: D 
  Date:   2019-05-23 (Thu, 23 May 2019)

  Changed paths:
M .mvn/jvm.config

  Log Message:
  ---
  Remove add module; use mvn dependencies instead


  Commit: c3f1a253d57eb37f5d5eca8179e5b9eeaa6d5416
  
https://github.com/cytoscape/cytoscape/commit/c3f1a253d57eb37f5d5eca8179e5b9eeaa6d5416
  Author: D 
  Date:   2019-07-16 (Tue, 16 Jul 2019)

  Changed paths:
M README.md

  Log Message:
  ---
  Merge branch 'develop' into java11


  Commit: 8683c11d3876b0f1d1053dbc5e98b8956130d101
  
https://github.com/cytoscape/cytoscape/commit/8683c11d3876b0f1d1053dbc5e98b8956130d101
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
A .travis.yml

  Log Message:
  ---
  Create .travis.yml


  Commit: 34ef7b5a73eaa43e549789c2a8f1b252c6e51435
  
https://github.com/cytoscape/cytoscape/commit/34ef7b5a73eaa43e549789c2a8f1b252c6e51435
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
A .travis.settings.xml

  Log Message:
  ---
  Create .travis.settings.xml


  Commit: b0edd99046cd4bf9929d9ce7b3f7c94b9630c7e3
  
https://github.com/cytoscape/cytoscape/commit/b0edd99046cd4bf9929d9ce7b3f7c94b9630c7e3
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Call cy.sh from travis


  Commit: 8d3c88ce7ba8d1daae921fe1c144dbdd2c7e94ee
  
https://github.com/cytoscape/cytoscape/commit/8d3c88ce7ba8d1daae921fe1c144dbdd2c7e94ee
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
A .mvn/jvm.config
A .travis.settings.xml
A .travis.yml

  Log Message:
  ---
  Merge branch 'java11' into develop


Compare: 
https://github.com/cytoscape/cytoscape/compare/7246d29f69dc...8d3c88ce7ba8

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[cytoscape/cytoscape-support] cb5a31: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-support
  Commit: cb5a31d3d15f923d5d6c88868a3286f7dcdddbc4
  
https://github.com/cytoscape/cytoscape-support/commit/cb5a31d3d15f923d5d6c88868a3286f7dcdddbc4
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-parent] 5d3dc6: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: 5d3dc61ef576df940c6cd16e5122f80dd20dfae9
  
https://github.com/cytoscape/cytoscape-parent/commit/5d3dc61ef576df940c6cd16e5122f80dd20dfae9
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-support] 826e5b: Update nexus repo references to ucsd

2019-08-19 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-support
  Commit: 826e5b7fe55a17e1baaaf6d6d065bf1a70883c15
  
https://github.com/cytoscape/cytoscape-support/commit/826e5b7fe55a17e1baaaf6d6d065bf1a70883c15
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Update nexus repo references to ucsd


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[cytoscape/cytoscape-parent] 8b2f8d: Rollback to 11.0.2 JavaDoc for travis

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: 8b2f8deac5505b464ad2a7006beaf8fbaf985130
  
https://github.com/cytoscape/cytoscape-parent/commit/8b2f8deac5505b464ad2a7006beaf8fbaf985130
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Rollback to 11.0.2 JavaDoc for travis


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[cytoscape/cytoscape-parent] 44f575: Enable javadoc plugin

2019-08-19 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: 44f57560b3ed29df372ddade980fb6f01a04b378
  
https://github.com/cytoscape/cytoscape-parent/commit/44f57560b3ed29df372ddade980fb6f01a04b378
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Enable javadoc plugin


  Commit: 8c60243df3a4512df2d23be83e3cc713b157e5c4
  
https://github.com/cytoscape/cytoscape-parent/commit/8c60243df3a4512df2d23be83e3cc713b157e5c4
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Merge branch 'java11-javadoc' into java11


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/bf0e4eaa69c6...8c60243df3a4

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[cytoscape/cytoscape-impl] 264f20: adding HelpTourTask, updating urls, http -> https ...

2019-08-19 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 264f208042e8ae72cc9070d6993bd7221dab9507
  
https://github.com/cytoscape/cytoscape-impl/commit/264f208042e8ae72cc9070d6993bd7221dab9507
  Author: Adam Treister 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M 
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpReportABugTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTaskFactory.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTask.java

  Log Message:
  ---
  adding HelpTourTask, updating urls, http -> https in chianti link


  Commit: 9954a1c2b511ed2e9d42837cae23287bf0c88cab
  
https://github.com/cytoscape/cytoscape-impl/commit/9954a1c2b511ed2e9d42837cae23287bf0c88cab
  Author: Adam Treister 
  Date:   2019-08-01 (Thu, 01 Aug 2019)

  Changed paths:
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpUserManualTask.java

  Log Message:
  ---
  https in manual.cytoscape.org link


  Commit: e1e1c622b77b7f2638aa682d9d5162cf50267be9
  
https://github.com/cytoscape/cytoscape-impl/commit/e1e1c622b77b7f2638aa682d9d5162cf50267be9
  Author: Scooter Morris 
  Date:   2019-08-09 (Fri, 09 Aug 2019)

  Changed paths:
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/internal/util/ViewUtil.java

  Log Message:
  ---
  Fix node drag


  Commit: d05678fb79b1ba8036bef23ac3e1cee4910f262c
  
https://github.com/cytoscape/cytoscape-impl/commit/d05678fb79b1ba8036bef23ac3e1cee4910f262c
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InputHandlerGlassPane.java
M 
ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/internal/util/ViewUtil.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpReportABugTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTask.java
A 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTourTaskFactory.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpTutorialsTask.java
M 
swing-application-impl/src/main/java/org/cytoscape/internal/view/help/HelpUserManualTask.java

  Log Message:
  ---
  Merge branch 'develop' into java11


Compare: 
https://github.com/cytoscape/cytoscape-impl/compare/d44e09ea7fed...d05678fb79b1

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[cytoscape/cytoscape-api] c275ae: Rollback to 11.0.2 JavaDoc for travis

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: c275aeb8ef1e1de52bde5705a0ce430cd5d5ee77
  
https://github.com/cytoscape/cytoscape-api/commit/c275aeb8ef1e1de52bde5705a0ce430cd5d5ee77
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Rollback to 11.0.2 JavaDoc for travis


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[cytoscape/cytoscape-app-template] 8fbcd8: Restore unpack-javadoc, update dependency plugin

2019-08-19 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-app-template
  Commit: 8fbcd8bebb777b140deab593e001dceb0159c96e
  
https://github.com/cytoscape/cytoscape-app-template/commit/8fbcd8bebb777b140deab593e001dceb0159c96e
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Restore unpack-javadoc, update dependency plugin


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[cytoscape/cytoscape-support] a2bfdd: Create .travis.settings.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-support
  Commit: a2bfdd05e76f4bc65511d2a9b83f28fe2b3faad9
  
https://github.com/cytoscape/cytoscape-support/commit/a2bfdd05e76f4bc65511d2a9b83f28fe2b3faad9
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
A .travis.settings.yml

  Log Message:
  ---
  Create .travis.settings.yml


  Commit: 02bcf41c5a6c507327d1a6214fc3e8baa3273c5c
  
https://github.com/cytoscape/cytoscape-support/commit/02bcf41c5a6c507327d1a6214fc3e8baa3273c5c
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
A .travis.yml

  Log Message:
  ---
  Create .travis.yml


  Commit: e4af724c330f61dd95f85de94bfdfd1a5f9b8489
  
https://github.com/cytoscape/cytoscape-support/commit/e4af724c330f61dd95f85de94bfdfd1a5f9b8489
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: a58b22c2b7e83dfb379f911d42aaa0dfe8200d35
  
https://github.com/cytoscape/cytoscape-support/commit/a58b22c2b7e83dfb379f911d42aaa0dfe8200d35
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
A .travis.settings.xml
R .travis.settings.yml

  Log Message:
  ---
  Rename .travis.settings.yml to .travis.settings.xml


  Commit: c092ae0f8108f7c79516a3a2b3b8eac6976f2fde
  
https://github.com/cytoscape/cytoscape-support/commit/c092ae0f8108f7c79516a3a2b3b8eac6976f2fde
  Author: dotasek 
  Date:   2019-08-06 (Tue, 06 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 826e5b7fe55a17e1baaaf6d6d065bf1a70883c15
  
https://github.com/cytoscape/cytoscape-support/commit/826e5b7fe55a17e1baaaf6d6d065bf1a70883c15
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Update nexus repo references to ucsd


  Commit: ff4f088997ccea9f0193682788054a53eeb0d456
  
https://github.com/cytoscape/cytoscape-support/commit/ff4f088997ccea9f0193682788054a53eeb0d456
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
A .travis.settings.xml
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Merge branch 'java11' into develop


Compare: 
https://github.com/cytoscape/cytoscape-support/compare/be50a1b9c222...ff4f088997cc

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[cytoscape/cytoscape-gui-distribution] 2f397f: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 2f397feda884b109e7dab04fad4d60a8d12252bd
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/2f397feda884b109e7dab04fad4d60a8d12252bd
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-impl] 1752aa: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 1752aabf616aba9eae02ebb3bb188e3a60f53262
  
https://github.com/cytoscape/cytoscape-impl/commit/1752aabf616aba9eae02ebb3bb188e3a60f53262
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-api] 0226f1: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 0226f13c05d9f6d2ede975d898ab74e6b7339378
  
https://github.com/cytoscape/cytoscape-api/commit/0226f13c05d9f6d2ede975d898ab74e6b7339378
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-api] d2446a: taglet refactor

2019-08-19 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  
https://github.com/cytoscape/cytoscape-api/commit/d2446a8e5ef6991ed38f7c0699c41b29b5505b48
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  taglet refactor


  Commit: 210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  
https://github.com/cytoscape/cytoscape-api/commit/210d5d968a5d7bf0c8b49362e261c55ac9e939b8
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Update javadoc link sources


  Commit: 00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  
https://github.com/cytoscape/cytoscape-api/commit/00b1e4d3d4cfb3d551246ffbb09885cb406ded56
  Author: D 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Uncomment taglets


  Commit: ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  
https://github.com/cytoscape/cytoscape-api/commit/ed32615bc8323cf2b0b8e179e52cae12ff2169fc
  Author: D 
  Date:   2019-08-14 (Wed, 14 Aug 2019)

  Changed paths:
M swing-application-api/pom.xml

  Log Message:
  ---
  Add javax as dependency


  Commit: cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  
https://github.com/cytoscape/cytoscape-api/commit/cdf9f90b128b42d4d2531e711148280cbfd5d6b8
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Switch to regular jar instead of aggregate jar for javadoc


  Commit: 15fec711bc28972b9e692c66430d097e95bd8f08
  
https://github.com/cytoscape/cytoscape-api/commit/15fec711bc28972b9e692c66430d097e95bd8f08
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M property-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Enable javadoc generation for swing-app-api


  Commit: 0cd2a105e3ded7534fd8d541d8178e675f38e676
  
https://github.com/cytoscape/cytoscape-api/commit/0cd2a105e3ded7534fd8d541d8178e675f38e676
  Author: D 
  Date:   2019-08-16 (Fri, 16 Aug 2019)

  Changed paths:
M app-api/pom.xml

  Log Message:
  ---
  Remove explicit links from javadoc (inherit intead)


  Commit: 154ddfc297b4a5438f2324446fa8eaf635c95d89
  
https://github.com/cytoscape/cytoscape-api/commit/154ddfc297b4a5438f2324446fa8eaf635c95d89
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M app-api/pom.xml
M pom.xml
M property-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  Merge branch 'java11-javadoc' into java11


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/90633763a6d6...154ddfc297b4

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[cytoscape/cytoscape-api] 42a2be: Update .travis.yml

2019-08-19 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 42a2be000802211f02b8c7c7e76cbeeae20732df
  
https://github.com/cytoscape/cytoscape-api/commit/42a2be000802211f02b8c7c7e76cbeeae20732df
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-gui-distribution] 60984a: Delete .travis.yml

2019-08-13 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 60984aa7b7be1195e7a017eac3e1f6bee159cbfa
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/60984aa7b7be1195e7a017eac3e1f6bee159cbfa
  Author: dotasek 
  Date:   2019-08-13 (Tue, 13 Aug 2019)

  Changed paths:
R .travis.yml

  Log Message:
  ---
  Delete .travis.yml


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[cytoscape/cytoscape-gui-distribution] 4ce724: Update cy-ndex-2 version

2019-08-21 Thread dotasek
  Branch: refs/heads/release/3.7.1
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 4ce724269eb557cd494da8af2b3c019d6a3714ba
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/4ce724269eb557cd494da8af2b3c019d6a3714ba
  Author: Unknown 
  Date:   2019-08-21 (Wed, 21 Aug 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Update cy-ndex-2 version


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[cytoscape/cytoscape-gui-distribution]

2019-08-21 Thread dotasek
  Branch: refs/tags/3.7.1
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-api] 154ddf: Merge branch 'java11-javadoc' into java11

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 154ddfc297b4a5438f2324446fa8eaf635c95d89
  
https://github.com/cytoscape/cytoscape-api/commit/154ddfc297b4a5438f2324446fa8eaf635c95d89
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M app-api/pom.xml
M pom.xml
M property-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  Merge branch 'java11-javadoc' into java11


  Commit: 3b842690d98912f21276a80dde13cc15a23aca31
  
https://github.com/cytoscape/cytoscape-api/commit/3b842690d98912f21276a80dde13cc15a23aca31
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
A .travis.settings.xml
M .travis.yml
M api-bundle/pom.xml
M app-api/pom.xml
M application-api/pom.xml
M ci-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M filter-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M pom.xml
M presentation-api/pom.xml
M property-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/ApiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/EnumClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/FinalClassTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/SpiInterfaceTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/StaticClassTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java
M util-api/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Merge branch 'java11' into develop


  Commit: 42a2be000802211f02b8c7c7e76cbeeae20732df
  
https://github.com/cytoscape/cytoscape-api/commit/42a2be000802211f02b8c7c7e76cbeeae20732df
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: 0226f13c05d9f6d2ede975d898ab74e6b7339378
  
https://github.com/cytoscape/cytoscape-api/commit/0226f13c05d9f6d2ede975d898ab74e6b7339378
  Author: dotasek 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: c275aeb8ef1e1de52bde5705a0ce430cd5d5ee77
  
https://github.com/cytoscape/cytoscape-api/commit/c275aeb8ef1e1de52bde5705a0ce430cd5d5ee77
  Author: D 
  Date:   2019-08-19 (Mon, 19 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Rollback to 11.0.2 JavaDoc for travis


  Commit: c897c00f0e4d60378f3c62ee9abe28b11ccbc6ad
  
https://github.com/cytoscape/cytoscape-api/commit/c897c00f0e4d60378f3c62ee9abe28b11ccbc6ad
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Merge branch 'develop' into java11-javadoc


  Commit: 858cd88d682536cd152d873282e595d38f414d38
  
https://github.com/cytoscape/cytoscape-api/commit/858cd88d682536cd152d873282e595d38f414d38
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  More permissive Javadoc version no hardcoded executable


Compare: 
https://github.com/cytoscape

[cytoscape/cytoscape-parent] beec4d: Merge branch 'develop' into java11-javadoc

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: beec4dc3fcd19897996ad00dfe7c21207542b7b9
  
https://github.com/cytoscape/cytoscape-parent/commit/beec4dc3fcd19897996ad00dfe7c21207542b7b9
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml
M pom.xml

  Log Message:
  ---
  Merge branch 'develop' into java11-javadoc


  Commit: 65cc87898d7e840aeffd422c04c4d26aa7ce2c70
  
https://github.com/cytoscape/cytoscape-parent/commit/65cc87898d7e840aeffd422c04c4d26aa7ce2c70
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  More permissive javadoc version


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/beec4dc3fcd1%5E...65cc87898d7e

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[cytoscape/cytoscape-api] 4acf2c: Update .travis.yml

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 4acf2c58a1e7579a4aa1234ed784269c8c1dd78d
  
https://github.com/cytoscape/cytoscape-api/commit/4acf2c58a1e7579a4aa1234ed784269c8c1dd78d
  Author: dotasek 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-api] edcf62: Disable fail on error for javadoc

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: edcf6222c3210e99489514e264f64152e1c9d18d
  
https://github.com/cytoscape/cytoscape-api/commit/edcf6222c3210e99489514e264f64152e1c9d18d
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Disable fail on error for javadoc


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[cytoscape/cytoscape-parent] beec4d: Merge branch 'develop' into java11-javadoc

2019-08-20 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: beec4dc3fcd19897996ad00dfe7c21207542b7b9
  
https://github.com/cytoscape/cytoscape-parent/commit/beec4dc3fcd19897996ad00dfe7c21207542b7b9
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml
M pom.xml

  Log Message:
  ---
  Merge branch 'develop' into java11-javadoc


  Commit: 65cc87898d7e840aeffd422c04c4d26aa7ce2c70
  
https://github.com/cytoscape/cytoscape-parent/commit/65cc87898d7e840aeffd422c04c4d26aa7ce2c70
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  More permissive javadoc version


  Commit: a82e3348ecc0b7badbcc6cddf2d3190eec7eac69
  
https://github.com/cytoscape/cytoscape-parent/commit/a82e3348ecc0b7badbcc6cddf2d3190eec7eac69
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Merge branch 'java11-javadoc' into develop


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/8b2f8deac550...a82e3348ecc0

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[cytoscape/cytoscape-api] a2d1c1: Remove disable-java8-doclint profile

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: a2d1c166109d010daeafacdc71e4177274f8c7e5
  
https://github.com/cytoscape/cytoscape-api/commit/a2d1c166109d010daeafacdc71e4177274f8c7e5
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M swing-app-api/pom.xml

  Log Message:
  ---
  Remove disable-java8-doclint profile

This profile is out of date; doclint is now disabled explicitly in javadoc 
creation.


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[cytoscape/cytoscape-api] f77a67: Try disabling doclint instead of fail on error

2019-08-20 Thread dotasek
  Branch: refs/heads/java11-javadoc
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: f77a677dda139ecce616bb45531c71321305bed0
  
https://github.com/cytoscape/cytoscape-api/commit/f77a677dda139ecce616bb45531c71321305bed0
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Try disabling doclint instead of fail on error


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[cytoscape/cytoscape-api] c897c0: Merge branch 'develop' into java11-javadoc

2019-08-20 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: c897c00f0e4d60378f3c62ee9abe28b11ccbc6ad
  
https://github.com/cytoscape/cytoscape-api/commit/c897c00f0e4d60378f3c62ee9abe28b11ccbc6ad
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Merge branch 'develop' into java11-javadoc


  Commit: 858cd88d682536cd152d873282e595d38f414d38
  
https://github.com/cytoscape/cytoscape-api/commit/858cd88d682536cd152d873282e595d38f414d38
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  More permissive Javadoc version no hardcoded executable


  Commit: 4acf2c58a1e7579a4aa1234ed784269c8c1dd78d
  
https://github.com/cytoscape/cytoscape-api/commit/4acf2c58a1e7579a4aa1234ed784269c8c1dd78d
  Author: dotasek 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


  Commit: edcf6222c3210e99489514e264f64152e1c9d18d
  
https://github.com/cytoscape/cytoscape-api/commit/edcf6222c3210e99489514e264f64152e1c9d18d
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Disable fail on error for javadoc


  Commit: f77a677dda139ecce616bb45531c71321305bed0
  
https://github.com/cytoscape/cytoscape-api/commit/f77a677dda139ecce616bb45531c71321305bed0
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Try disabling doclint instead of fail on error


  Commit: a2d1c166109d010daeafacdc71e4177274f8c7e5
  
https://github.com/cytoscape/cytoscape-api/commit/a2d1c166109d010daeafacdc71e4177274f8c7e5
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M swing-app-api/pom.xml

  Log Message:
  ---
  Remove disable-java8-doclint profile

This profile is out of date; doclint is now disabled explicitly in javadoc 
creation.


  Commit: 81ef41cdd2b35aad0fe7e04d585f4bde394e255c
  
https://github.com/cytoscape/cytoscape-api/commit/81ef41cdd2b35aad0fe7e04d585f4bde394e255c
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml
M app-api/pom.xml
M swing-app-api/pom.xml

  Log Message:
  ---
  Merge branch 'java11-javadoc' into develop


  Commit: 46454729356a7c37979f9feb6e7cc785bdccee12
  
https://github.com/cytoscape/cytoscape-api/commit/46454729356a7c37979f9feb6e7cc785bdccee12
  Author: D 
  Date:   2019-08-20 (Tue, 20 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Build using develop on travis


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/c275aeb8ef1e...46454729356a

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[cytoscape/cytoscape-api] 848d37: Re-implement taglets

2019-08-26 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 848d37b443d36862c92be182a0d900dc67858543
  
https://github.com/cytoscape/cytoscape-api/commit/848d37b443d36862c92be182a0d900dc67858543
  Author: D 
  Date:   2019-08-26 (Mon, 26 Aug 2019)

  Changed paths:
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/AbstractApiTaglet.java
M 
taglets/src/main/java/org/cytoscape/taglets/compatibility/InModuleTaglet.java
M 
taglets/src/test/java/org/cytoscape/taglets/compatibility/AbstractTagletTester.java

  Log Message:
  ---
  Re-implement taglets

See CYTOSCAPE-12529


  Commit: 1944da76da18501a7c2fc72e537809d622045edc
  
https://github.com/cytoscape/cytoscape-api/commit/1944da76da18501a7c2fc72e537809d622045edc
  Author: D 
  Date:   2019-08-26 (Mon, 26 Aug 2019)

  Changed paths:
M swing-util-api/src/main/java/org/cytoscape/util/swing/TextIcon.java

  Log Message:
  ---
  Merge remote-tracking branch 'origin/develop' into develop


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/2e3437062489...1944da76da18

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[cytoscape/cytoscape-gui-distribution] 1c66c5: Update install4j plugin, auto-sign mac DMGs

2019-09-03 Thread dotasek
  Branch: refs/heads/release/3.7.1
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 1c66c59f4eec765ba59db5931b56750370fff02c
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/1c66c59f4eec765ba59db5931b56750370fff02c
  Author: dotasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  Update install4j plugin, auto-sign mac DMGs


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[cytoscape/cytoscape-gui-distribution] c01c53: Set mac signing file in Cytoscape.install4j

2019-09-03 Thread dotasek
  Branch: refs/heads/release/3.7.1
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: c01c53ff55f0c9a971656b3bf161739d930d3df2
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/c01c53ff55f0c9a971656b3bf161739d930d3df2
  Author: dotasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M packaging/src/main/install4j/Cytoscape.install4j

  Log Message:
  ---
  Set mac signing file in Cytoscape.install4j


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[cytoscape/cytoscape-gui-distribution] 673316: Update install4j location for weekly build server

2019-08-29 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 673316dfb89311c0c457ada055cc8502d911d417
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/673316dfb89311c0c457ada055cc8502d911d417
  Author: dotasek 
  Date:   2019-08-29 (Thu, 29 Aug 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  Update install4j location for weekly build server


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[cytoscape/cytoscape-gui-distribution] 0b8aa9: Update install4j executable for new build machine

2019-08-27 Thread dotasek
  Branch: refs/heads/release/3.7.1
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 0b8aa90a35b2baf52b0df73b47bf61307a8066d8
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/0b8aa90a35b2baf52b0df73b47bf61307a8066d8
  Author: dotasek 
  Date:   2019-08-27 (Tue, 27 Aug 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  Update install4j executable for new build machine


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[cytoscape/cytoscape-impl] 78da01: Add missing imports

2019-08-22 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 78da0170339cf8bb02967811e8bf27999dd5aec6
  
https://github.com/cytoscape/cytoscape-impl/commit/78da0170339cf8bb02967811e8bf27999dd5aec6
  Author: D 
  Date:   2019-08-22 (Thu, 22 Aug 2019)

  Changed paths:
M 
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/view/editor/mappingeditor/ContinuousTrackRenderer.java

  Log Message:
  ---
  Add missing imports


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[cytoscape/cytoscape-admin-scripts] dc9ff6: Updated system-checker for version 3.7.2

2019-09-05 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-admin-scripts
  Commit: dc9ff6485ab474d2e65ecc45eef5998dc1ffac07
  
https://github.com/cytoscape/cytoscape-admin-scripts/commit/dc9ff6485ab474d2e65ecc45eef5998dc1ffac07
  Author: D 
  Date:   2019-09-05 (Thu, 05 Sep 2019)

  Changed paths:
M system-checker/linux.sh
M system-checker/mac.sh
M system-checker/windows.bat

  Log Message:
  ---
  Updated system-checker for version 3.7.2


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[cytoscape/cytoscape-app-template] 665587: Update to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-app-template
  Commit: 665587b8b86b02f8bbb9397690dc5c559f771620
  
https://github.com/cytoscape/cytoscape-app-template/commit/665587b8b86b02f8bbb9397690dc5c559f771620
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: 1bd9c12a5a07db5471bba4017f33c9aba2b86941
  
https://github.com/cytoscape/cytoscape-app-template/commit/1bd9c12a5a07db5471bba4017f33c9aba2b86941
  Author: Brett Settle 
  Date:   2018-12-12 (Wed, 12 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Switch version to 3.7.1


  Commit: ed570847c3f2e14e9ebb46eb7b533e3704ac6613
  
https://github.com/cytoscape/cytoscape-app-template/commit/ed570847c3f2e14e9ebb46eb7b533e3704ac6613
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update version to 3.7.2


Compare: 
https://github.com/cytoscape/cytoscape-app-template/compare/937d64c9c0fe...ed570847c3f2

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[cytoscape/cytoscape-parent] 5b6f00: Update version to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: 5b6f0071b06887fa821951318e54f86327d56fd3
  
https://github.com/cytoscape/cytoscape-parent/commit/5b6f0071b06887fa821951318e54f86327d56fd3
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update version to 3.7.1-SNAPSHOT


  Commit: 98da7b52c84708de4d308b4a0451de580d5467fe
  
https://github.com/cytoscape/cytoscape-parent/commit/98da7b52c84708de4d308b4a0451de580d5467fe
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: 69b7444632793c2195d0f773667f5790abc6ca66
  
https://github.com/cytoscape/cytoscape-parent/commit/69b7444632793c2195d0f773667f5790abc6ca66
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: 7860609e0ddc2f25142e8a030b3e9cad1783c0f6
  
https://github.com/cytoscape/cytoscape-parent/commit/7860609e0ddc2f25142e8a030b3e9cad1783c0f6
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Update version to 3.7.2


Compare: 
https://github.com/cytoscape/cytoscape-parent/compare/1ef3191c0c6b...7860609e0ddc

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[cytoscape/cytoscape] deb08e: Added run-all command to cy.sh

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape
  Commit: deb08ef49f4cdf180d7bc0a09437355a19c26ee3
  
https://github.com/cytoscape/cytoscape/commit/deb08ef49f4cdf180d7bc0a09437355a19c26ee3
  Author: Brett Settle 
  Date:   2018-12-10 (Mon, 10 Dec 2018)

  Changed paths:
M cy.sh

  Log Message:
  ---
  Added run-all command to cy.sh


  Commit: 2100b3d6106ed35329377cc45ebe33052f1e8e8e
  
https://github.com/cytoscape/cytoscape/commit/2100b3d6106ed35329377cc45ebe33052f1e8e8e
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: a3e5e65497a0e868429146df1a709ab5595f7f1f
  
https://github.com/cytoscape/cytoscape/commit/a3e5e65497a0e868429146df1a709ab5595f7f1f
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M cy.sh

  Log Message:
  ---
  Updated run-all command


  Commit: 1e7d694878330e4dd47ddc9b893fbeb1284a4564
  
https://github.com/cytoscape/cytoscape/commit/1e7d694878330e4dd47ddc9b893fbeb1284a4564
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
A build_output.txt
M pom.xml

  Log Message:
  ---
  Update version to 3.7.2


  Commit: 151a4a2ffbbb98584ce408fe8d7ee2d3afd11d32
  
https://github.com/cytoscape/cytoscape/commit/151a4a2ffbbb98584ce408fe8d7ee2d3afd11d32
  Author: David Otasek 
  Date:   2019-09-04 (Wed, 04 Sep 2019)

  Changed paths:
A build_output.txt
M cy.sh
M pom.xml

  Log Message:
  ---
  Resolved merge conflict, kept 3.7.1 changes


Compare: 
https://github.com/cytoscape/cytoscape/compare/bc89195c494b...151a4a2ffbbb

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[cytoscape/cytoscape-gui-distribution] 5ee176: Update to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 5ee176ca8ce80eeae1a5d03571482254de9757a1
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/5ee176ca8ce80eeae1a5d03571482254de9757a1
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M application-metadata-impl/pom.xml
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.bat
M assembly/src/main/bin/cytoscape.sh
M branding/pom.xml
M cmdline-impl/pom.xml
M diagnostics/pom.xml
M features/pom.xml
M integration-test/pom.xml
M launcher/pom.xml
M packaging/pom.xml
M pom.xml
M splash-launcher/pom.xml
M splash-updater-impl/pom.xml
M third-party/pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: 7c98d2c2a2d760f464566b7e66201a480c6cd3c6
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/7c98d2c2a2d760f464566b7e66201a480c6cd3c6
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M application-metadata-impl/pom.xml
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.bat
M assembly/src/main/bin/cytoscape.sh
M branding/pom.xml
M cmdline-impl/pom.xml
M diagnostics/pom.xml
M features/pom.xml
M integration-test/pom.xml
M launcher/pom.xml
M packaging/pom.xml
M pom.xml
M splash-launcher/pom.xml
M splash-updater-impl/pom.xml
M third-party/pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: 4ce724269eb557cd494da8af2b3c019d6a3714ba
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/4ce724269eb557cd494da8af2b3c019d6a3714ba
  Author: Unknown 
  Date:   2019-08-21 (Wed, 21 Aug 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Update cy-ndex-2 version


  Commit: 0b8aa90a35b2baf52b0df73b47bf61307a8066d8
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/0b8aa90a35b2baf52b0df73b47bf61307a8066d8
  Author: dotasek 
  Date:   2019-08-27 (Tue, 27 Aug 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  Update install4j executable for new build machine


  Commit: 1c66c59f4eec765ba59db5931b56750370fff02c
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/1c66c59f4eec765ba59db5931b56750370fff02c
  Author: dotasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  Update install4j plugin, auto-sign mac DMGs


  Commit: c01c53ff55f0c9a971656b3bf161739d930d3df2
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/c01c53ff55f0c9a971656b3bf161739d930d3df2
  Author: dotasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M packaging/src/main/install4j/Cytoscape.install4j

  Log Message:
  ---
  Set mac signing file in Cytoscape.install4j


  Commit: 75b08cffcf1e876dfd4a9a2fe0d6e826043ccbcb
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/75b08cffcf1e876dfd4a9a2fe0d6e826043ccbcb
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M application-metadata-impl/pom.xml
M assembly/pom.xml
M assembly/src/main/bin/cytoscape.bat
M assembly/src/main/bin/cytoscape.sh
M branding/pom.xml
M cmdline-impl/pom.xml
M diagnostics/pom.xml
M features/pom.xml
M integration-test/pom.xml
M launcher/pom.xml
M packaging/pom.xml
M pom.xml
M splash-launcher/pom.xml
M splash-updater-impl/pom.xml
M third-party/pom.xml

  Log Message:
  ---
  Update version to 3.7.2


Compare: 
https://github.com/cytoscape/cytoscape-gui-distribution/compare/562e731fba8e...75b08cffcf1e

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[cytoscape/cytoscape-impl] f66c10: Update to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: f66c10e6d639d62f0f144912b97478e0d15dbd11
  
https://github.com/cytoscape/cytoscape-impl/commit/f66c10e6d639d62f0f144912b97478e0d15dbd11
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M app-impl/pom.xml
M application-impl/pom.xml
M command-executor-impl/pom.xml
M core-task-impl/pom.xml
M datasource-impl/pom.xml
M ding-impl/ding-presentation-impl/pom.xml
M ding-impl/performance-debug/pom.xml
M ding-impl/pom.xml
M edge-bundler-impl/pom.xml
M editor-impl/pom.xml
M equations-functions-impl/pom.xml
M equations-impl/pom.xml
M event-impl/impl/pom.xml
M event-impl/it/pom.xml
M event-impl/pom.xml
M filter-impl/pom.xml
M filter2-impl/pom.xml
M graphml-impl/pom.xml
M group-impl/pom.xml
M gui-cmdline-parser-impl/pom.xml
M headless-application-impl/pom.xml
M headless-cmdline-parser-impl/pom.xml
M io-impl/impl/pom.xml
M io-impl/performance/pom.xml
M io-impl/pom.xml
M jobs-impl/pom.xml
M layout-cytoscape-impl/pom.xml
M layout-impl/pom.xml
M layout-jgraph-impl/pom.xml
M layout-prefuse-impl/pom.xml
M linkout-impl/pom.xml
M log-swing-impl/pom.xml
M manual-layout-impl/pom.xml
M model-impl/impl/pom.xml
M model-impl/it/pom.xml
M model-impl/performance-debug/pom.xml
M model-impl/performance/pom.xml
M model-impl/pom.xml
M model-impl/table-performance-debug/pom.xml
M pom.xml
M presentation-impl/pom.xml
M property-impl/pom.xml
M scripting-impl/pom.xml
M search-impl/pom.xml
M session-impl/impl/pom.xml
M session-impl/integration-test/pom.xml
M session-impl/pom.xml
M swing-application-impl/pom.xml
M swing-util-impl/pom.xml
M table-browser-impl/pom.xml
M table-import-impl/pom.xml
M util-impl/pom.xml
M viewmodel-impl/impl/pom.xml
M viewmodel-impl/it/pom.xml
M viewmodel-impl/pom.xml
M vizmap-gui-core-impl/pom.xml
M vizmap-gui-impl/pom.xml
M vizmap-impl/impl/pom.xml
M vizmap-impl/it/pom.xml
M vizmap-impl/pom.xml
M webservice-impl/pom.xml
M work-headless-impl/pom.xml
M work-impl/pom.xml
M work-swing-impl/impl/pom.xml
M work-swing-impl/it/pom.xml
M work-swing-impl/pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: c324874f2ced8cb61b003676349cb3ae79c883cf
  
https://github.com/cytoscape/cytoscape-impl/commit/c324874f2ced8cb61b003676349cb3ae79c883cf
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M app-impl/pom.xml
M application-impl/pom.xml
M command-executor-impl/pom.xml
M core-task-impl/pom.xml
M datasource-impl/pom.xml
M ding-impl/ding-presentation-impl/pom.xml
M ding-impl/performance-debug/pom.xml
M ding-impl/pom.xml
M edge-bundler-impl/pom.xml
M editor-impl/pom.xml
M equations-functions-impl/pom.xml
M equations-impl/pom.xml
M event-impl/impl/pom.xml
M event-impl/it/pom.xml
M event-impl/pom.xml
M filter-impl/pom.xml
M filter2-impl/pom.xml
M graphml-impl/pom.xml
M group-impl/pom.xml
M gui-cmdline-parser-impl/pom.xml
M headless-application-impl/pom.xml
M headless-cmdline-parser-impl/pom.xml
M io-impl/impl/pom.xml
M io-impl/performance/pom.xml
M io-impl/pom.xml
M jobs-impl/pom.xml
M layout-cytoscape-impl/pom.xml
M layout-impl/pom.xml
M layout-jgraph-impl/pom.xml
M layout-prefuse-impl/pom.xml
M linkout-impl/pom.xml
M log-swing-impl/pom.xml
M manual-layout-impl/pom.xml
M model-impl/impl/pom.xml
M model-impl/it/pom.xml
M model-impl/performance-debug/pom.xml
M model-impl/performance/pom.xml
M model-impl/pom.xml
M model-impl/table-performance-debug/pom.xml
M pom.xml
M presentation-impl/pom.xml
M property-impl/pom.xml
M scripting-impl/pom.xml
M search-impl/pom.xml
M session-impl/impl/pom.xml
M session-impl/integration-test/pom.xml
M session-impl/pom.xml
M swing-application-impl/pom.xml
M swing-util-impl/pom.xml
M table-browser-impl/pom.xml
M table-import-impl/pom.xml
M util-impl/pom.xml
M viewmodel-impl/impl/pom.xml
M viewmodel-impl/it/pom.xml
M viewmodel-impl/pom.xml
M vizmap-gui-core-impl/pom.xml
M vizmap-gui-impl/pom.xml
M vizmap-impl/impl/pom.xml
M vizmap-impl/it/pom.xml
M vizmap-impl/pom.xml
M webservice-impl/pom.xml
M work-headless-impl/pom.xml
M work-impl/pom.xml
M work-swing-impl/impl/pom.xml
M work-swing-impl/it/pom.xml
M work-swing-impl/pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: 480abfc792ec55f576243d0414a97ecc26fa49e2
  
https://github.com/cytoscape/cytoscape-impl/commit/480abfc792ec55f576243d0414a97ecc26fa49e2
  Author: Unknown 
  Date:   2018-12-19 (Wed, 19 Dec 2018)

  Changed paths:
M 

[cytoscape/cytoscape-api] 97804a: Update to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-api
  Commit: 97804af93d7d8d55a03f113b2d29fbe55f5f0950
  
https://github.com/cytoscape/cytoscape-api/commit/97804af93d7d8d55a03f113b2d29fbe55f5f0950
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M api-bundle/pom.xml
M app-api/pom.xml
M application-api/pom.xml
M ci-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M filter-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M pom.xml
M presentation-api/pom.xml
M property-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M util-api/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: ca39186ac5a145d779d518e7aeaa5476a2ccca12
  
https://github.com/cytoscape/cytoscape-api/commit/ca39186ac5a145d779d518e7aeaa5476a2ccca12
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M api-bundle/pom.xml
M app-api/pom.xml
M application-api/pom.xml
M ci-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M filter-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M pom.xml
M presentation-api/pom.xml
M property-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M util-api/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: b47ad5b79b8e5b1b967d6c15aa12f61357948daa
  
https://github.com/cytoscape/cytoscape-api/commit/b47ad5b79b8e5b1b967d6c15aa12f61357948daa
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M api-bundle/pom.xml
M app-api/pom.xml
M application-api/pom.xml
M ci-api/pom.xml
M command-executor-api/pom.xml
M core-task-api/pom.xml
M datasource-api/pom.xml
M equations-api/pom.xml
M event-api/pom.xml
M filter-api/pom.xml
M group-api/pom.xml
M io-api/pom.xml
M jobs-api/pom.xml
M layout-api/pom.xml
M model-api/pom.xml
M pom.xml
M presentation-api/pom.xml
M property-api/pom.xml
M service-api/pom.xml
M session-api/pom.xml
M swing-app-api/pom.xml
M swing-application-api/pom.xml
M swing-util-api/pom.xml
M taglets/pom.xml
M util-api/pom.xml
M viewmodel-api/pom.xml
M vizmap-api/pom.xml
M vizmap-gui-api/pom.xml
M webservice-api/pom.xml
M webservice-swing-api/pom.xml
M work-api/pom.xml
M work-swing-api/pom.xml

  Log Message:
  ---
  Update version to 3.7.2


Compare: 
https://github.com/cytoscape/cytoscape-api/compare/e22f40ff030f...b47ad5b79b8e

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[cytoscape/cytoscape-support] dadfce: Update to 3.7.1-SNAPSHOT

2019-09-04 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-support
  Commit: dadfce8dafa55c25466fc4ede5f3e78e78391223
  
https://github.com/cytoscape/cytoscape-support/commit/dadfce8dafa55c25466fc4ede5f3e78e78391223
  Author: Unknown 
  Date:   2018-12-07 (Fri, 07 Dec 2018)

  Changed paths:
M archetypes/api-provider-app/pom.xml
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/pom.xml
M archetypes/task-app/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/cmdline/pom.xml
M launch-framework/launcher/pom.xml
M launch-framework/pom.xml
M launch-framework/startlevel-assembly/pom.xml
M pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Update to 3.7.1-SNAPSHOT


  Commit: 7fb3246e8d90f48a424c225fbd1a48f0a65384a6
  
https://github.com/cytoscape/cytoscape-support/commit/7fb3246e8d90f48a424c225fbd1a48f0a65384a6
  Author: Brett Settle 
  Date:   2018-12-13 (Thu, 13 Dec 2018)

  Changed paths:
M archetypes/api-provider-app/pom.xml
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/pom.xml
M archetypes/task-app/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/cmdline/pom.xml
M launch-framework/launcher/pom.xml
M launch-framework/pom.xml
M launch-framework/startlevel-assembly/pom.xml
M pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Switch\ to\ 3.7.1


  Commit: ea8c4b0ca17e374a638c0d76de2151003912cd63
  
https://github.com/cytoscape/cytoscape-support/commit/ea8c4b0ca17e374a638c0d76de2151003912cd63
  Author: David Otasek 
  Date:   2019-09-03 (Tue, 03 Sep 2019)

  Changed paths:
M archetypes/api-provider-app/pom.xml
M archetypes/api-provider-app/src/main/resources/archetype-resources/pom.xml
M archetypes/cyaction-app/pom.xml
M archetypes/cyaction-app/src/main/resources/archetype-resources/pom.xml
M archetypes/meta-app/pom.xml
M archetypes/meta-app/src/main/resources/archetype-resources/pom.xml
M archetypes/pom.xml
M archetypes/task-app/pom.xml
M archetypes/task-app/src/main/resources/archetype-resources/pom.xml
M cy-commons-cli/pom.xml
M integration-test-support/pom.xml
M launch-framework/cmdline/pom.xml
M launch-framework/launcher/pom.xml
M launch-framework/pom.xml
M launch-framework/startlevel-assembly/pom.xml
M pom.xml
M task-testing-impl/pom.xml

  Log Message:
  ---
  Update version to 3.7.2


Compare: 
https://github.com/cytoscape/cytoscape-support/compare/454e39894462...ea8c4b0ca17e

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[cytoscape/cytoscape-api]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-api

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[cytoscape/cytoscape]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape

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[cytoscape/cytoscape-impl]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-impl

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[cytoscape/cytoscape-api]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-api

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[cytoscape/cytoscape-gui-distribution]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-support]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-support

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[cytoscape/cytoscape-support]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-support

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[cytoscape/cytoscape-app-template]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-app-template

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[cytoscape/cytoscape]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape

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[cytoscape/cytoscape-parent]

2019-09-04 Thread dotasek
  Branch: refs/tags/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-parent

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[cytoscape/cytoscape-app-template]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-app-template

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[cytoscape/cytoscape-gui-distribution]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-impl]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-impl

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[cytoscape/cytoscape-parent]

2019-09-04 Thread dotasek
  Branch: refs/heads/release/3.7.2
  Home:   https://github.com/cytoscape/cytoscape-parent

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[cytoscape/cytoscape-gui-distribution] 1c1ef8: Add $KARAF_HOME to specs locator in startup

2019-09-06 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 1c1ef878d5c48c812259be6332601deee64e68fd
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/1c1ef878d5c48c812259be6332601deee64e68fd
  Author: D 
  Date:   2019-09-06 (Fri, 06 Sep 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Add $KARAF_HOME to specs locator in startup


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[cytoscape/cytoscape-parent] 728efc: Remove master branch from travis build

2019-09-12 Thread dotasek
  Branch: refs/heads/master
  Home:   https://github.com/cytoscape/cytoscape-parent
  Commit: 728efcada67e9810ca4f27f91363cf7617847713
  
https://github.com/cytoscape/cytoscape-parent/commit/728efcada67e9810ca4f27f91363cf7617847713
  Author: dotasek 
  Date:   2019-09-12 (Thu, 12 Sep 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Remove master branch from travis build


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[cytoscape/cytoscape-gui-distribution] f1e9d5: Fix exe4j execution

2019-09-12 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: f1e9d5f72ef2523c8946c0266143108dadbde460
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/f1e9d5f72ef2523c8946c0266143108dadbde460
  Author: D 
  Date:   2019-09-12 (Thu, 12 Sep 2019)

  Changed paths:
M packaging/src/main/install4j/Cytoscape.install4j

  Log Message:
  ---
  Fix exe4j execution


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[cytoscape/cytoscape-gui-distribution] 3cba9e: Update pom.xml

2019-09-10 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 3cba9e470c3af6e79bcc3b250a045bd669a11c12
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/3cba9e470c3af6e79bcc3b250a045bd669a11c12
  Author: dotasek 
  Date:   2019-09-10 (Tue, 10 Sep 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Update pom.xml


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[cytoscape/cytoscape-gui-distribution] 84c4f7: Update cy-ndex-2 version

2019-09-11 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 84c4f7ab3626e3085c56b0e729860af6d3b11ece
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/84c4f7ab3626e3085c56b0e729860af6d3b11ece
  Author: Unknown 
  Date:   2019-09-11 (Wed, 11 Sep 2019)

  Changed paths:
M assembly/pom.xml

  Log Message:
  ---
  Update cy-ndex-2 version


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[cytoscape/cytoscape-gui-distribution] d363cf: CherryPick install4j plugin update

2019-09-11 Thread dotasek
  Branch: refs/heads/develop
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: d363cfd9d2dcc2dfd28c8432bb3652f4bfe73c6b
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/d363cfd9d2dcc2dfd28c8432bb3652f4bfe73c6b
  Author: D 
  Date:   2019-09-11 (Wed, 11 Sep 2019)

  Changed paths:
M packaging/pom.xml

  Log Message:
  ---
  CherryPick install4j plugin update


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[cytoscape/cytoscape-gui-distribution]

2019-07-30 Thread dotasek
  Branch: refs/tags/untagged-796392b35712e8e5290f
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-gui-distribution] 16d781: Add windows assembly to github releases

2019-07-30 Thread dotasek
  Branch: refs/heads/travis-ci
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 16d78140fa1a1183b033271e59b38247959e802c
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/16d78140fa1a1183b033271e59b38247959e802c
  Author: dotasek 
  Date:   2019-07-30 (Tue, 30 Jul 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Add windows assembly to github releases


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[cytoscape/cytoscape-gui-distribution]

2019-07-30 Thread dotasek
  Branch: refs/tags/untagged-af3f45a4886922782c21
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-gui-distribution] 13b52e: secure API key

2019-07-30 Thread dotasek
  Branch: refs/heads/travis-ci
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 13b52e94a9246030558d595013a6ebb1f00bce97
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/13b52e94a9246030558d595013a6ebb1f00bce97
  Author: Unknown 
  Date:   2019-07-30 (Tue, 30 Jul 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  secure API key


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[cytoscape/cytoscape-gui-distribution] 3e99ec: add skip_cleanup

2019-07-30 Thread dotasek
  Branch: refs/heads/travis-ci
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 3e99ecc92142b9a4df3fcfee02744785fb005878
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/3e99ecc92142b9a4df3fcfee02744785fb005878
  Author: Unknown 
  Date:   2019-07-30 (Tue, 30 Jul 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  add skip_cleanup


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[cytoscape/cytoscape-gui-distribution] 163168: Remove download chatter from CI logging

2019-07-30 Thread dotasek
  Branch: refs/heads/travis-ci
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution
  Commit: 163168249d67438f4a995a8496acc19f8df222f8
  
https://github.com/cytoscape/cytoscape-gui-distribution/commit/163168249d67438f4a995a8496acc19f8df222f8
  Author: dotasek 
  Date:   2019-07-30 (Tue, 30 Jul 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Remove download chatter from CI logging


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[cytoscape/cytoscape-gui-distribution]

2019-07-30 Thread dotasek
  Branch: refs/tags/untagged-796392b35712e8e5290f
  Home:   https://github.com/cytoscape/cytoscape-gui-distribution

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[cytoscape/cytoscape-impl] b5d80f: Repair failing test

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: b5d80f6cde42da15f2eff1e11ed3fa2823e9e184
  
https://github.com/cytoscape/cytoscape-impl/commit/b5d80f6cde42da15f2eff1e11ed3fa2823e9e184
  Author: D 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M 
io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkReaderTest.java

  Log Message:
  ---
  Repair failing test


  Commit: 76ef7c2e89927d8f59f37bf79d7cea91cc35df63
  
https://github.com/cytoscape/cytoscape-impl/commit/76ef7c2e89927d8f59f37bf79d7cea91cc35df63
  Author: D 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M 
core-task-impl/src/test/java/org/cytoscape/task/internal/hide/HideUtilsTest.java
M 
table-browser-impl/src/test/java/org/cytoscape/browser/internal/view/BrowserTableTest.java

  Log Message:
  ---
  Ignore failing tests


  Commit: 962543eae944095baaa73061cea1c982bdd5e099
  
https://github.com/cytoscape/cytoscape-impl/commit/962543eae944095baaa73061cea1c982bdd5e099
  Author: D 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M app-impl/pom.xml
M application-impl/pom.xml
M command-executor-impl/pom.xml
M core-task-impl/pom.xml
M ding-impl/ding-presentation-impl/pom.xml
M edge-bundler-impl/pom.xml
M editor-impl/pom.xml
M equations-impl/pom.xml
M event-impl/pom.xml
M filter-impl/pom.xml
M filter2-impl/pom.xml
M group-impl/pom.xml
M gui-cmdline-parser-impl/pom.xml
M headless-application-impl/pom.xml
M headless-cmdline-parser-impl/pom.xml
M io-impl/pom.xml
M jobs-impl/pom.xml
M layout-cytoscape-impl/pom.xml
M layout-impl/pom.xml
M layout-jgraph-impl/pom.xml
M layout-prefuse-impl/pom.xml
M log-swing-impl/pom.xml
M manual-layout-impl/pom.xml
M model-impl/pom.xml
M presentation-impl/pom.xml
M property-impl/pom.xml
M search-impl/pom.xml
M session-impl/impl/pom.xml
M swing-application-impl/pom.xml
M swing-util-impl/pom.xml
M table-browser-impl/pom.xml
M table-import-impl/pom.xml
M util-impl/pom.xml
M viewmodel-impl/pom.xml
M vizmap-gui-core-impl/pom.xml
M vizmap-impl/pom.xml
M webservice-impl/pom.xml
M work-headless-impl/pom.xml
M work-impl/pom.xml
M work-swing-impl/pom.xml

  Log Message:
  ---
  Update repository references to ucsd nexus


Compare: 
https://github.com/cytoscape/cytoscape-impl/compare/29546cb0fb30...962543eae944

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[cytoscape/cytoscape-impl] 50d082: Create .travis.settings.xml

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 50d082760fa3b1291e2edceaaf6d15bd28d36ad0
  
https://github.com/cytoscape/cytoscape-impl/commit/50d082760fa3b1291e2edceaaf6d15bd28d36ad0
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
A .travis.settings.xml

  Log Message:
  ---
  Create .travis.settings.xml


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[cytoscape/cytoscape-impl] 43d682: Update .travis.yml

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 43d682b491431bdfd1c7dfb3928284d4275a7957
  
https://github.com/cytoscape/cytoscape-impl/commit/43d682b491431bdfd1c7dfb3928284d4275a7957
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-impl] cf93d9: Update .travis.yml

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: cf93d9342c67a41b1ef383d1691dd39a5aa75668
  
https://github.com/cytoscape/cytoscape-impl/commit/cf93d9342c67a41b1ef383d1691dd39a5aa75668
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-impl] e17671: Make travis build skip initial install

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: e17671853ac8ecaee1d624e96867bad90e6eee2d
  
https://github.com/cytoscape/cytoscape-impl/commit/e17671853ac8ecaee1d624e96867bad90e6eee2d
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Make travis build skip initial install


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[cytoscape/cytoscape-impl] 13a223: Update .travis.yml

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: 13a2234680ca7a08e7e218ab7d878469b4e7529f
  
https://github.com/cytoscape/cytoscape-impl/commit/13a2234680ca7a08e7e218ab7d878469b4e7529f
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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[cytoscape/cytoscape-impl] b28751: Update .travis.yml

2019-08-07 Thread dotasek
  Branch: refs/heads/java11
  Home:   https://github.com/cytoscape/cytoscape-impl
  Commit: b287517b293d83a7a3ae0133d8c0dac69843c912
  
https://github.com/cytoscape/cytoscape-impl/commit/b287517b293d83a7a3ae0133d8c0dac69843c912
  Author: dotasek 
  Date:   2019-08-07 (Wed, 07 Aug 2019)

  Changed paths:
M .travis.yml

  Log Message:
  ---
  Update .travis.yml


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