Major refactoring of jmzTab to make it slim.

bigbio · Aug 18, 2021 · aa23b4a · aa23b4a
1 parent dc98047
commit aa23b4a
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Showing 2 changed files with 18 additions and 21 deletions.
diff --git a/assembly.xml b/assembly.xml
@@ -1,5 +1,5 @@
 <assembly>
-  <id>genome-deployment</id>
+  <id>pepgenome-deployment</id>
 
   <formats>
     <format>zip</format>
@@ -10,7 +10,7 @@
   <dependencySets>
     <dependencySet>
       <useProjectArtifact>false</useProjectArtifact>
-      <outputDirectory>lib</outputDirectory>
+<!--      <outputDirectory>lib</outputDirectory>-->
       <unpack>false</unpack>
       <scope>runtime</scope>
       <outputFileNameMapping>${artifact.artifactId}-${artifact.baseVersion}.${artifact.extension}</outputFileNameMapping>

diff --git a/pom.xml b/pom.xml
@@ -1,12 +1,11 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 
-
   <modelVersion>4.0.0</modelVersion>
 
   <groupId>io.github.bigbio</groupId>
   <artifactId>pepgenome</artifactId>
-  <version>1.1.0-SNAPSHOT</version>
+  <version>1.1.1</version>
   <packaging>jar</packaging>
   <name>Pepgenome: Peptide to Genome Coordinates</name>
   <url>https://github.com/bigbio/pepgenome/</url>
@@ -54,7 +53,6 @@
     <jmztab.version>3.0.5</jmztab.version>
   </properties>
 
-
   <dependencies>
     <!-- mzIdentML File dependencies -->
     <dependency>
@@ -73,7 +71,7 @@
     <dependency>
       <groupId>io.github.bigbio.external</groupId>
       <artifactId>pia</artifactId>
-      <version>1.3.18</version>
+      <version>1.3.20</version>
       <exclusions>
         <exclusion>
           <groupId>commons-cli</groupId>
@@ -179,17 +177,16 @@
         <version>3.1.2</version>
         <configuration>
           <excludes>
-            <exclude>src/test</exclude>
-            <exclude>src/test/*.class</exclude>
+            <exclude>src/test/**</exclude>
           </excludes>
           <archive>
             <index>true</index>
             <manifest>
-              <!-- Adds the classpath to the created manifest -->
-              <addClasspath>true</addClasspath>
-              <classpathPrefix>lib/</classpathPrefix>
-              <!-- Configures the main class of the application -->
-              <mainClass>de.mpc.pia.modeller.PIAModeller</mainClass>
+<!--              &lt;!&ndash; Adds the classpath to the created manifest &ndash;&gt;-->
+<!--              <addClasspath>true</addClasspath>-->
+<!--              <classpathPrefix>lib/</classpathPrefix>-->
+<!--              &lt;!&ndash; Configures the main class of the application &ndash;&gt;-->
+              <mainClass>org.bigbio.pgatk.pepgenome.PepGenomeTool</mainClass>
             </manifest>
           </archive>
         </configuration>
@@ -278,21 +275,21 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-gpg-plugin</artifactId>
-        <version>1.6</version>
+        <version>3.0.1</version>
+        <configuration>
+          <!-- Prevent `gpg` from using pinentry programs -->
+          <gpgArguments>
+            <arg>--pinentry-mode</arg>
+            <arg>loopback</arg>
+          </gpgArguments>
+        </configuration>
         <executions>
           <execution>
             <id>sign-artifacts</id>
             <phase>verify</phase>
             <goals>
               <goal>sign</goal>
             </goals>
-            <configuration>
-              <!-- Prevent `gpg` from using pinentry programs -->
-              <gpgArguments>
-                <arg>--pinentry-mode</arg>
-                <arg>loopback</arg>
-              </gpgArguments>
-            </configuration>
           </execution>
         </executions>
       </plugin>