Prepare 0.7.7 release.

Pre-publish the new DOI. Update the NEWS file. Also update the README file to mention the CLI (instead of only the core library and the ROBOT plugin) at the top. Update all copyright notices of files that were edited in 2024.
gouttegd · Apr 28, 2024 · 747b1a0 · 747b1a0
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,9 +8,9 @@ authors:
 license: GPL-3.0-or-later
 url: "https://incenp.org/dvlpt/sssom-java/"
 repository-code: "https://github.com/gouttegd/sssom-java"
-version: 0.7.6
-date-released: "2024-03-27"
-doi: 10.5281/zenodo.10888082
+version: 0.7.7
+date-released: "2024-04-28"
+doi: 10.5281/zenodo.11080540
 references:
   - authors:
       - family-names: "Matentzoglu"

diff --git a/NEWS b/NEWS
@@ -1,3 +1,15 @@
+Changes in sssom-java-0.7.7
+---------------------------
+
+    * SSSOM/TSV writer:
+      * Align the format of floating numbers with SSSOM-Py.
+      * Remove propagated values from set-level metadata.
+    * xref-extract:
+      * Fill the subject_source field with the ontology IRI.
+      * Accept multiple spaces in the --map-prefix-to-predicate option.
+    * sssom-cli:
+      * New --update-from-ontology option.
+
 Changes in sssom-java-0.7.6
 ---------------------------
 

diff --git a/README.md b/README.md
@@ -10,9 +10,10 @@ Ontology Mappings
 for the Java language – just a hobby, won’t be big and professional like
 `sssom-py`.
 
-The project provides both a Java library that can be used to support
-the SSSOM standard in a Java application, and a pluggable command for
-the [ROBOT](http://robot.obolibrary.org/) ontology manipulation tool.
+The project provides a Java library that can be used to support the
+SSSOM standard in a Java application, a program to manipulate mapping
+sets from the command line, and a pluggable command for the
+[ROBOT](http://robot.obolibrary.org/) ontology manipulation tool.
 
 Features
 --------

diff --git a/cli/src/main/java/org/incenp/obofoundry/sssom/cli/MetadataMerger.java b/cli/src/main/java/org/incenp/obofoundry/sssom/cli/MetadataMerger.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/cli/src/main/java/org/incenp/obofoundry/sssom/cli/SimpleCLI.java b/cli/src/main/java/org/incenp/obofoundry/sssom/cli/SimpleCLI.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/cli/src/test/java/org/incenp/obofoundry/sssom/cli/SSSOMCLITest.java b/cli/src/test/java/org/incenp/obofoundry/sssom/cli/SSSOMCLITest.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/ExtendedPrefixMap.java b/core/src/main/java/org/incenp/obofoundry/sssom/ExtendedPrefixMap.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/ExtraMetadataPolicy.java b/core/src/main/java/org/incenp/obofoundry/sssom/ExtraMetadataPolicy.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/MatchTermTypeConverter.java b/core/src/main/java/org/incenp/obofoundry/sssom/MatchTermTypeConverter.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/SlotHelper.java b/core/src/main/java/org/incenp/obofoundry/sssom/SlotHelper.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/SlotPropagator.java b/core/src/main/java/org/incenp/obofoundry/sssom/SlotPropagator.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/SlotVisitor.java b/core/src/main/java/org/incenp/obofoundry/sssom/SlotVisitor.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/SlotVisitorBase.java b/core/src/main/java/org/incenp/obofoundry/sssom/SlotVisitorBase.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/TSVReader.java b/core/src/main/java/org/incenp/obofoundry/sssom/TSVReader.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/YAMLConverter.java b/core/src/main/java/org/incenp/obofoundry/sssom/YAMLConverter.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/model/BuiltinPrefix.java b/core/src/main/java/org/incenp/obofoundry/sssom/model/BuiltinPrefix.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/model/MappingCardinality.java b/core/src/main/java/org/incenp/obofoundry/sssom/model/MappingCardinality.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/owl/AnnotationAxiomGenerator.java b/core/src/main/java/org/incenp/obofoundry/sssom/owl/AnnotationAxiomGenerator.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/owl/AnnotationVisitor.java b/core/src/main/java/org/incenp/obofoundry/sssom/owl/AnnotationVisitor.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/owl/XrefExtractor.java b/core/src/main/java/org/incenp/obofoundry/sssom/owl/XrefExtractor.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/transform/MappingFormatter.java b/core/src/main/java/org/incenp/obofoundry/sssom/transform/MappingFormatter.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/main/java/org/incenp/obofoundry/sssom/transform/NamedMappingTransformer.java b/core/src/main/java/org/incenp/obofoundry/sssom/transform/NamedMappingTransformer.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/test/java/org/incenp/obofoundry/sssom/ExtendedPrefixMapTest.java b/core/src/test/java/org/incenp/obofoundry/sssom/ExtendedPrefixMapTest.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/test/java/org/incenp/obofoundry/sssom/SlotPropagatorTest.java b/core/src/test/java/org/incenp/obofoundry/sssom/SlotPropagatorTest.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/core/src/test/java/org/incenp/obofoundry/sssom/transform/SSSOMTransformReaderTest.java b/core/src/test/java/org/incenp/obofoundry/sssom/transform/SSSOMTransformReaderTest.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/robot/src/main/java/org/incenp/obofoundry/sssom/robot/XrefExtractCommand.java b/robot/src/main/java/org/incenp/obofoundry/sssom/robot/XrefExtractCommand.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by

diff --git a/robot/src/test/java/org/incenp/obofoundry/sssom/robot/SSSOMInjectionCommandTest.java b/robot/src/test/java/org/incenp/obofoundry/sssom/robot/SSSOMInjectionCommandTest.java
@@ -1,6 +1,6 @@
 /*
  * SSSOM-Java - SSSOM library for Java
- * Copyright © 2023 Damien Goutte-Gattat
+ * Copyright © 2023,2024 Damien Goutte-Gattat
  * 
  * This program is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by