Merge pull request #245 from matthiaskoenig/develop

Changes for release v0.2.6
matthiaskoenig · Oct 3, 2017 · ddb086b · ddb086b
2 parents f17465a + 7811723
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diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# ![alt tag](./docs/images/logo100.png) cy3sbml - SBML for Cytoscape 3
+# ![alt tag](https://github.com/matthiaskoenig/cy3sbml/raw/develop/docs/images/logo100.png) cy3sbml - SBML for Cytoscape 3
 
 [![DOI](https://zenodo.org/badge/5066/matthiaskoenig/cy3sbml.svg)](https://zenodo.org/badge/latestdoi/5066/matthiaskoenig/cy3sbml)
 <a href="https://www.paypal.com/cgi-bin/webscr?cmd=_s-xclick&amp;hosted_button_id=RYHNRJFBMWD5N" title="Donate to this project using Paypal"><img src="https://img.shields.io/badge/paypal-donate-yellow.svg" alt="PayPal donate button" /></a>
@@ -32,7 +32,7 @@ like [BioModels](http://www.biomodels.org) and one-click access to annotation re
 * Support of qual, comp and fbc extensions
 * Provides access to RDF based annotation information within
   the network context (and non-RDF annotations)
-* Tested with all models from sbml-test-suite (3.2.0), Biomodels (release 30) and BiGG models (v1.2)
+* Tested with all models from sbml-test-suite (3.2.0), Biomodels (release 30) and BiGG models (v1.3)
 
 For Cytoscape 2 use [cy2sbml](https://github.com/matthiaskoenig/cy2sbml) with documentation available from http://matthiaskoenig.github.io/cy2sbml/
 
@@ -51,7 +51,8 @@ Matthias König is supported by the Federal Ministry of Education and Research (
 ## Installation
 ### Install
 cy3sbml is available via the [Cytoscape App Store](http://apps.cytoscape.org/apps/cy3sbml).  
-* install the latest version of [Cytoscape](http://www.cytoscape.org/) (>=3.4) 
+* install the latest version of [Cytoscape](http://www.cytoscape.org/) (>=3.5.1) 
+
 * In Cytoscape open `Apps → App Manager → Install Apps` and search for `cy3sbml`. 
 * Select `cy3sbml` and click install.
 
@@ -81,7 +82,10 @@ The `cy3sbml-vx.x.x.jar` if available in the `target` folder.
 More detailed build instructions are available from https://goo.gl/4xMgff.
 
 ## Changelog
-**v0.2.5** [2016/06/20]
+**v0.2.6** [?]
+
+**v0.2.5** [2016/06/19]
+
 * Bug fixes
 * Updated UniProt Information
 * Updated HTML display
@@ -255,4 +259,4 @@ below.
 [Apache Taverna Language](https://github.com/apache/incubator-taverna-language) [![License (Apache 2.0)](https://img.shields.io/badge/license-Apache2-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0) [checked 2016-08-16]
 
 ----
-&copy; 2016 Matthias König. Developed and maintained by Matthias König, Andreas Dräger and Nicolas Rodriguez.
+&copy; 2017 Matthias König. Developed and maintained by Matthias König, Andreas Dräger and Nicolas Rodriguez.
diff --git a/docs/specifications/sbml.L3V1.core-R1.pdf b/docs/specifications/sbml.L3V1.core-R1.pdf
diff --git a/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar b/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar
diff --git a/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar.md5 b/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar.md5
@@ -1 +1 @@
-0c268224b7c2d2f1e9c593fd70ba9f3b
+9ad4a061fb634b6fce7e348bf5b5603b
diff --git a/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar.sha1 b/lib/cy3sbml-dep/jsbml-comp/1.0-b1/jsbml-comp-1.0-b1.jar.sha1
@@ -1 +1 @@
-bdedcf4aff3c7b37d404fc2224db9ff606bbaaea
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diff --git a/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>1.0-b1</version>
     </versions>
-    <lastUpdated>20170619141914</lastUpdated>
+    <lastUpdated>20171003195203</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml.md5
@@ -1 +1 @@
-bd6cb31b5bf5bead85a622a018e7d2ac
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diff --git a/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-comp/maven-metadata-local.xml.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar b/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar
diff --git a/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar.md5 b/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar.sha1 b/lib/cy3sbml-dep/jsbml-distrib/0.5/jsbml-distrib-0.5.jar.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>0.5</version>
     </versions>
-    <lastUpdated>20170619141920</lastUpdated>
+    <lastUpdated>20171003195207</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml.md5
@@ -1 +1 @@
-2c762ace95280b7036af8f47e6bac8b8
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diff --git a/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-distrib/maven-metadata-local.xml.sha1
@@ -1 +1 @@
-f7fe4bc7b65d19187389b848f50f8d36b8448faa
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diff --git a/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar b/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar
diff --git a/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar.md5 b/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar.sha1 b/lib/cy3sbml-dep/jsbml-fbc/1.0-b1/jsbml-fbc-1.0-b1.jar.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>1.0-b1</version>
     </versions>
-    <lastUpdated>20170619141916</lastUpdated>
+    <lastUpdated>20171003195205</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml.md5
@@ -1 +1 @@
-84985dbd6420279ea0dccb781c3e7325
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diff --git a/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-fbc/maven-metadata-local.xml.sha1
@@ -1 +1 @@
-c96d83e430cbb104a8e57fa998026ea48e1170e4
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diff --git a/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar b/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar
diff --git a/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar.md5 b/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar.md5
@@ -1 +1 @@
-10cb03d6a1283e6a92f405d45b4b40e2
+bd1967b357f802d9a061d594fb8de21c
diff --git a/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar.sha1 b/lib/cy3sbml-dep/jsbml-groups/0.4-b1/jsbml-groups-0.4-b1.jar.sha1
@@ -1 +1 @@
-61f95561a3a925781dd439b8e4020223dd0d39f9
+3006b5977cd2e538645220f151b6957ecdf3e0eb
diff --git a/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>0.4-b1</version>
     </versions>
-    <lastUpdated>20170619141918</lastUpdated>
+    <lastUpdated>20171003195206</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml.md5
@@ -1 +1 @@
-f8eae029ea1f3c304eb882d73ec69572
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diff --git a/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-groups/maven-metadata-local.xml.sha1
@@ -1 +1 @@
-48b212e4bd3a78d22ad59efdc1b3ef943e66111b
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diff --git a/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar b/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar
diff --git a/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar.md5 b/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar.md5
@@ -1 +1 @@
-93414de94b32ec4ba1450da41d68b550
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diff --git a/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar.sha1 b/lib/cy3sbml-dep/jsbml-layout/1.0-b1/jsbml-layout-1.0-b1.jar.sha1
@@ -1 +1 @@
-bcba66bf549388d744b431426516907576f49518
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diff --git a/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>1.0-b1</version>
     </versions>
-    <lastUpdated>20170619141913</lastUpdated>
+    <lastUpdated>20171003195202</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-layout/maven-metadata-local.xml.sha1
@@ -1 +1 @@
-8af6613559ba44a9fc502c75099024c208f81acf
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diff --git a/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar b/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar
diff --git a/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar.md5 b/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar.sha1 b/lib/cy3sbml-dep/jsbml-qual/2.1-b1/jsbml-qual-2.1-b1.jar.sha1
@@ -1 +1 @@
-985c7778c1e6278c16ab73e065f77b14f302e384
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diff --git a/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>2.1-b1</version>
     </versions>
-    <lastUpdated>20170619141911</lastUpdated>
+    <lastUpdated>20171003195201</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-qual/maven-metadata-local.xml.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar b/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar
diff --git a/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar.md5 b/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar.sha1 b/lib/cy3sbml-dep/jsbml-tidy/1.2.1/jsbml-tidy-1.2.1.jar.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml
@@ -7,6 +7,6 @@
     <versions>
       <version>1.2.1</version>
     </versions>
-    <lastUpdated>20170619141922</lastUpdated>
+    <lastUpdated>20171003195209</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml-tidy/maven-metadata-local.xml.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar
diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar.md5 b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar.sha1 b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/jsbml-1.3-SNAPSHOT.jar.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml
@@ -7,17 +7,17 @@
     <snapshot>
       <localCopy>true</localCopy>
     </snapshot>
-    <lastUpdated>20170619141909</lastUpdated>
+    <lastUpdated>20171003195159</lastUpdated>
     <snapshotVersions>
       <snapshotVersion>
         <extension>jar</extension>
         <value>1.3-SNAPSHOT</value>
-        <updated>20170619141909</updated>
+        <updated>20171003195159</updated>
       </snapshotVersion>
       <snapshotVersion>
         <extension>pom</extension>
         <value>1.3-SNAPSHOT</value>
-        <updated>20170619141909</updated>
+        <updated>20171003195159</updated>
       </snapshotVersion>
     </snapshotVersions>
   </versioning>

diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml/1.3-SNAPSHOT/maven-metadata-local.xml.sha1
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml b/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml
@@ -6,6 +6,6 @@
     <versions>
       <version>1.3-SNAPSHOT</version>
     </versions>
-    <lastUpdated>20170619141909</lastUpdated>
+    <lastUpdated>20171003195159</lastUpdated>
   </versioning>
 </metadata>
diff --git a/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml.md5 b/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml.md5
@@ -1 +1 @@
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diff --git a/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml.sha1 b/lib/cy3sbml-dep/jsbml/maven-metadata-local.xml.sha1
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		46d552842b879573fc724050f4dc147dfb560958
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		@@ -1 +1 @@
		8d2c1855b4d0f151be3c7ecb3d923721
		c171ee02a80a642598acbe50f3b67f96
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		a9ac2ed6d0634f126b08a1d207910fd06cea9f5e
		38004faa88f1e585be227ca608fa75e75bad21d0