Set version to 2.0.4, update changelog.

monarch-initiative · Nov 20, 2023 · 4fdfd30 · 4fdfd30
1 parent 2a5291d
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,6 +6,18 @@ Changelog
 latest
 ------
 
+-----
+2.0.4
+-----
+
+Minor release, no breaking changes.
+
+- Fix broken implementation of `MinimalOntology.subOntology` method.
+- Simplify implementation of CSR adjacency matrix that backs `OntologyGraph` by default.
+- Improve `OntologyGraph` test coverage.
+- Add microbenchmark to benchmark the ontology loading.
+- Update dependencies, remove Guava usage.
+
 ------
 2.0.3
 ------

diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@ associate phenotype annotation files.
 
 - **Language/Platform:** Java >=11
 - **License:** BSD 3-Clause Clear
-- **Version:** 2.0.3
+- **Version:** 2.0.4
 - **Authors:**
     - Sebastian Bauer
     - Peter N. Robinson
@@ -39,7 +39,7 @@ We recommend indicating the phenol version in the `properties` section of the po
 ```
 <properties>
   (...)
-  <phenol.version>2.0.3</phenol.version>
+  <phenol.version>2.0.4</phenol.version>
 </properties>
 ```
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -12,7 +12,7 @@
 # The short X.Y version.
 version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.3'
+release = '2.0.4'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

diff --git a/phenol-analysis/pom.xml b/phenol-analysis/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-analysis</artifactId>

diff --git a/phenol-annotations/pom.xml b/phenol-annotations/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-annotations</artifactId>

diff --git a/phenol-cli/pom.xml b/phenol-cli/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-cli</artifactId>

diff --git a/phenol-cli/src/main/java/org/monarchinitiative/phenol/cli/Main.java b/phenol-cli/src/main/java/org/monarchinitiative/phenol/cli/Main.java
@@ -9,7 +9,7 @@
 
 @CommandLine.Command(name = "phenol demo",
   mixinStandardHelpOptions = true,
-  version = "2.0.3",
+  version = "2.0.4",
   description = "phenol demo programs")
 public class Main implements Callable<Integer> {
   private static final Logger LOGGER = LoggerFactory.getLogger(Main.class);

diff --git a/phenol-core/pom.xml b/phenol-core/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-core</artifactId>

diff --git a/phenol-io/pom.xml b/phenol-io/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <groupId>org.monarchinitiative.phenol</groupId>
     <artifactId>phenol</artifactId>
-    <version>2.0.4-SNAPSHOT</version>
+    <version>2.0.4</version>
   </parent>
 
   <artifactId>phenol-io</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
   <groupId>org.monarchinitiative.phenol</groupId>
   <artifactId>phenol</artifactId>
   <packaging>pom</packaging>
-  <version>2.0.4-SNAPSHOT</version>
+  <version>2.0.4</version>
 
   <name>Phenol</name>