debian/changelog

+beast-mcmc (1.10.4+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Migrating to libejml-java 0.38.
+
+ -- Andrius Merkys <merkys@debian.org>  Tue, 21 May 2019 05:27:43 -0400
+
 beast-mcmc (1.10.4+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/control

@@ -22,7 +22,7 @@ Build-Depends: debhelper (>= 11~),
                junit4,
                libmtj-java,
                libitext1-java,
-               libejml-java,
+               libejml-java (>= 0.38),
                libjlapack-java
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc

debian/patches/fix_classpath_in_build_xml.patch

@@ -13,7 +13,7 @@ Forwarded: no
      <property name="dist" location="${build}/dist"/>
  
      <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
-@@ -48,6 +49,21 @@
+@@ -48,6 +49,31 @@
  
      <path id="classpath">
          <fileset dir="${lib}" includes="**/*.jar"/>
@@ -31,11 +31,21 @@ Forwarded: no
 +        <fileset dir="${deblib}" includes="mtj.jar"/>
 +        <fileset dir="${deblib}" includes="options.jar"/>
 +        <fileset dir="${deblib}" includes="EJML.jar"/>
++        <fileset dir="${deblib}" includes="ejml-all.jar"/>
++        <fileset dir="${deblib}" includes="ejml-all.jar"/>
++        <fileset dir="${deblib}" includes="ejml-cdense.jar"/>
++        <fileset dir="${deblib}" includes="ejml-core.jar"/>
++        <fileset dir="${deblib}" includes="ejml-ddense.jar"/>
++        <fileset dir="${deblib}" includes="ejml-dsparse.jar"/>
++        <fileset dir="${deblib}" includes="ejml-experimental.jar"/>
++        <fileset dir="${deblib}" includes="ejml-fdense.jar"/>
++        <fileset dir="${deblib}" includes="ejml-simple.jar"/>
++        <fileset dir="${deblib}" includes="ejml-zdense.jar"/>
 +        <fileset dir="${deblib}" includes="jlapack-lapack.jar"/>
      </path>
  
      <!-- start -->
-@@ -159,17 +175,6 @@
+@@ -161,17 +187,6 @@
                  <include name="org/virion/jam/**/*.png"/>
                  <include name="dr/**/*.properties"/>
              </fileset>
@@ -53,7 +63,7 @@ Forwarded: no
          </jar>
  
          <!-- Put everything in ${build} into the beauti.jar file -->
-@@ -226,11 +231,6 @@
+@@ -228,11 +243,6 @@
              <fileset dir="${src}">
                  <include name="dr/**/*.png"/>
              </fileset>
@@ -67,7 +77,7 @@ Forwarded: no
          <!-- Put everything in ${build} into the trace.jar file -->
 --- a/.classpath
 +++ b/.classpath
-@@ -1,20 +1,18 @@
+@@ -1,20 +1,27 @@
  <?xml version="1.0" encoding="UTF-8"?>
  <classpath>
  	<classpathentry kind="src" path="src"/>
@@ -98,6 +108,15 @@ Forwarded: no
 +	<classpathentry kind="lib" path="/usr/share/java/mtj.jar"/>
 +	<classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
 +	<classpathentry kind="lib" path="/usr/share/java/EJML.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-all.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-cdense.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-core.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-ddense.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-dsparse.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-experimental.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-fdense.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-simple.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/ejml-zdense.jar"/>
 +	<classpathentry kind="lib" path="/usr/share/java/jlapack-lapack.jar"/>
  	<classpathentry kind="output" path="bin"/>
  </classpath>

debian/patches/series

@@ -3,3 +3,4 @@ fix_classpath_in_build_xml.patch
 create_soname.patch
 fix_encoding.patch
 ignore_mac_install.patch
+update-ejml.patch