Release v1.0.0-RC2

monarch-initiative · Jul 12, 2021 · 4f8530e · 4f8530e
1 parent f779b23
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,11 +2,24 @@
 Changelog
 =========
 
+
+----------
+v1.0.0-RC2
+----------
+
+- Implement VCF output format
+- Clean up the repo from the obsolete code
+- Improve documentation & test coverage
+- Bug fixes
+  - remove null pointer in ``GeneService``
+  - do not run coverage filter if the coverage data is missing for a variant
+
+
 ----------
 v1.0.0-RC1
 ----------
 
-- Rename `annotate` CLI command to `prioritize`
+- Rename ``annotate`` CLI command to ``prioritize``
 - Multiple minor adjustments
 
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -56,7 +56,7 @@
 # The short X.Y version.
 version = u'1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'1.0.0-RC1'
+release = u'1.0.0-RC2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/pom.xml b/pom.xml
@@ -18,7 +18,7 @@
         <module>svanna-benchmark</module>
     </modules>
     <groupId>org.jax.svanna</groupId>
-    <version>1.0.0-RC2-SNAPSHOT</version>
+    <version>1.0.0-RC2</version>
     <name>SvAnna</name>
 
     <parent>

diff --git a/svanna-benchmark/pom.xml b/svanna-benchmark/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java b/svanna-benchmark/src/main/java/org/jax/svanna/benchmark/Main.java
@@ -15,11 +15,11 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer>  {
 
-    public static final String VERSION = "svanna-benchmark v1.0.0-RC1-SNAPSHOT";
+    public static final String VERSION = "svanna-benchmark v1.0.0-RC2";
 
     public static final int WIDTH = 120;
 
-    public static final String FOOTER = "See the full documentation at `https://github.com/TheJacksonLaboratory/SvAnna`";
+    public static final String FOOTER = "See the full documentation at `https://svanna.readthedocs.io/en/v1.0.0-rc2`";
 
     private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder()
             .commands(bold, fg_blue, underline)

diff --git a/svanna-cli/pom.xml b/svanna-cli/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>svanna-cli</artifactId>

diff --git a/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java b/svanna-cli/src/main/java/org/jax/svanna/cli/Main.java
@@ -18,11 +18,11 @@
         footer = Main.FOOTER)
 public class Main implements Callable<Integer>  {
 
-    public static final String VERSION = "svanna-cli v1.0.0-RC1";
+    public static final String VERSION = "svanna-cli v1.0.0-RC2";
 
     public static final int WIDTH = 120;
 
-    public static final String FOOTER = "See the full documentation at `https://github.com/TheJacksonLaboratory/SvAnna`";
+    public static final String FOOTER = "See the full documentation at `https://svanna.readthedocs.io/en/v1.0.0-rc2`";
 
     private static final CommandLine.Help.ColorScheme COLOR_SCHEME = new CommandLine.Help.ColorScheme.Builder()
             .commands(bold, fg_blue, underline)

diff --git a/svanna-core/pom.xml b/svanna-core/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-db/pom.xml b/svanna-db/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-ingest/pom.xml b/svanna-ingest/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>svanna-ingest</artifactId>

diff --git a/svanna-io/pom.xml b/svanna-io/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-spring-boot-autoconfigure/pom.xml b/svanna-spring-boot-autoconfigure/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-spring-boot-starter/pom.xml b/svanna-spring-boot-starter/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/svanna-test/pom.xml b/svanna-test/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>SvAnna</artifactId>
         <groupId>org.jax.svanna</groupId>
-        <version>1.0.0-RC2-SNAPSHOT</version>
+        <version>1.0.0-RC2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>