From b50de88251d710caa5053b57455efe81ac474e1a Mon Sep 17 00:00:00 2001
From: Walter <walterxie@users.noreply.github.com>
Date: Thu, 19 Sep 2024 13:33:49 +1200
Subject: [PATCH] Release 1.2.0 #66

---
 phylonco-beast/pom.xml                                   | 2 +-
 phylonco-beast/src/assembly/phylonco-beast-assembly.xml  | 9 +++++++++
 phylonco-beast/version.xml                               | 4 ++--
 phylonco-lphy-studio/pom.xml                             | 2 +-
 .../src/assembly/phylonco-lphy-studio-assembly.xml       | 1 +
 phylonco-lphy/pom.xml                                    | 2 +-
 .../src/main/java/phylonco/lphy/spi/PhyloncoImpl.java    | 8 ++++----
 phylonco-lphybeast/pom.xml                               | 2 +-
 phylonco-lphybeast/version.xml                           | 4 ++--
 9 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/phylonco-beast/pom.xml b/phylonco-beast/pom.xml
index c7e0133..03841e5 100644
--- a/phylonco-beast/pom.xml
+++ b/phylonco-beast/pom.xml
@@ -9,7 +9,7 @@
 
     <artifactId>phylonco-beast</artifactId>
     <!-- must be consisting with version.xml   -->
-    <version>1.2.0-SNAPSHOT</version>
+    <version>1.2.0</version>
 
     <properties>
         <beastVersion>2.7.6</beastVersion>
diff --git a/phylonco-beast/src/assembly/phylonco-beast-assembly.xml b/phylonco-beast/src/assembly/phylonco-beast-assembly.xml
index afbd9cc..0687eb0 100644
--- a/phylonco-beast/src/assembly/phylonco-beast-assembly.xml
+++ b/phylonco-beast/src/assembly/phylonco-beast-assembly.xml
@@ -31,6 +31,15 @@
             </sources>
         </moduleSet>
     </moduleSets>
+    <fileSets>
+        <fileSet>
+            <directory>../examples</directory>
+            <outputDirectory>examples</outputDirectory>
+            <excludes>
+                <exclude>test_read_count_model.xml</exclude>
+            </excludes>
+        </fileSet>
+    </fileSets>
     <files>
         <file>
             <source>version.xml</source>
diff --git a/phylonco-beast/version.xml b/phylonco-beast/version.xml
index 0d32010..9e9f8ca 100644
--- a/phylonco-beast/version.xml
+++ b/phylonco-beast/version.xml
@@ -35,8 +35,8 @@
         <provider classname="phylonco.beast.evolution.populationmodel.GompertzGrowth_t50"/>
         <provider classname="phylonco.beast.evolution.populationmodel.ConstantGrowth"/>
         <provider classname="phylonco.beast.evolution.populationmodel.StochasticVariableSelection"/>
-        <provider classname="phylonco.beast.evolution.readcountmodel.LikelihoodReadCountModel"/>
-        <provider classname="phylonco.beast.evolution.datatype.ReadCount"/>
+<!--        <provider classname="phylonco.beast.evolution.readcountmodel.LikelihoodReadCountModel"/>-->
+<!--        <provider classname="phylonco.beast.evolution.datatype.ReadCount"/>-->
     </service>
 
 </package>
diff --git a/phylonco-lphy-studio/pom.xml b/phylonco-lphy-studio/pom.xml
index 1a573d4..3b84dcb 100644
--- a/phylonco-lphy-studio/pom.xml
+++ b/phylonco-lphy-studio/pom.xml
@@ -7,7 +7,7 @@
     </parent>
 
     <artifactId>phylonco-lphy-studio</artifactId>
-    <version>1.2.0-SNAPSHOT</version>
+    <version>1.2.0</version>
 
     <dependencies>
         <dependency>
diff --git a/phylonco-lphy-studio/src/assembly/phylonco-lphy-studio-assembly.xml b/phylonco-lphy-studio/src/assembly/phylonco-lphy-studio-assembly.xml
index 9e90112..51597fe 100644
--- a/phylonco-lphy-studio/src/assembly/phylonco-lphy-studio-assembly.xml
+++ b/phylonco-lphy-studio/src/assembly/phylonco-lphy-studio-assembly.xml
@@ -48,6 +48,7 @@
                 <include>**/data/**</include>
             </includes>
             <excludes>
+                <exclude>**/gt16ReadCountModel.lphy</exclude>
                 <exclude>**/todo/**</exclude>
                 <exclude>**/*.log</exclude>
                 <exclude>**/*.trees</exclude>
diff --git a/phylonco-lphy/pom.xml b/phylonco-lphy/pom.xml
index 14a1c4f..d21ca21 100644
--- a/phylonco-lphy/pom.xml
+++ b/phylonco-lphy/pom.xml
@@ -8,7 +8,7 @@
     </parent>
 
     <artifactId>phylonco-lphy</artifactId>
-    <version>1.2.0-SNAPSHOT</version>
+    <version>1.2.0</version>
 
     <dependencies>
         <dependency>
diff --git a/phylonco-lphy/src/main/java/phylonco/lphy/spi/PhyloncoImpl.java b/phylonco-lphy/src/main/java/phylonco/lphy/spi/PhyloncoImpl.java
index 11dfdd0..a33e722 100644
--- a/phylonco-lphy/src/main/java/phylonco/lphy/spi/PhyloncoImpl.java
+++ b/phylonco-lphy/src/main/java/phylonco/lphy/spi/PhyloncoImpl.java
@@ -35,10 +35,10 @@ public PhyloncoImpl() {
     public List<Class<? extends GenerativeDistribution>> declareDistributions() {
         return Arrays.asList(
                 GT16ErrorModel.class,
-                HomozygousAlignmentDistribution.class,
-                ReadCountModel.class,
-                PloidyModel.class,
-                CoverageModel.class);
+                HomozygousAlignmentDistribution.class);
+//                ReadCountModel.class,
+//                PloidyModel.class,
+//                CoverageModel.class);
     }
 
     @Override
diff --git a/phylonco-lphybeast/pom.xml b/phylonco-lphybeast/pom.xml
index 053c1e1..24fbd94 100644
--- a/phylonco-lphybeast/pom.xml
+++ b/phylonco-lphybeast/pom.xml
@@ -8,7 +8,7 @@
 
     <artifactId>phylonco-lphybeast</artifactId>
     <!-- must be consisting with version.xml   -->
-    <version>1.2.0-SNAPSHOT</version>
+    <version>1.2.0</version>
 
     <dependencies>
 <!--        <dependency>-->
diff --git a/phylonco-lphybeast/version.xml b/phylonco-lphybeast/version.xml
index 293e67d..c69f2af 100644
--- a/phylonco-lphybeast/version.xml
+++ b/phylonco-lphybeast/version.xml
@@ -1,9 +1,9 @@
 <package name='phylonco.lphybeast' version='1.2.0'>
     <!-- phylonco beast -->
     <depends on='phylonco' atleast='1.2.0'/>
-<!--    <depends on='lphybeast' atleast='1.2.0'/>-->
+    <depends on='lphybeast' atleast='1.2.0'/>
 <!--  include lphybeast  -->
-    <depends on='lphybeast-flc' atleast='0.0.1'/>
+<!--    <depends on='lphybeast-flc' atleast='0.0.1'/>-->
 
     <!-- add BEAST2 service below  -->
     <service type="beast.base.evolution.datatype.DataType">