[med-svn] [Git][med-team/beast-mcmc][master] 3 commits: Refresh ignore_mac_install.patch.

[Andrius Merkys (@merkys)]

Andrius Merkys pushed to branch master at Debian Med / beast-mcmc


Commits:
db2abd62 by Andrius Merkys at 2022-11-24T01:59:31-05:00
Refresh ignore_mac_install.patch.

- - - - -
db8a3380 by Andrius Merkys at 2022-11-24T02:20:09-05:00
Adjust update-ejml.patch to build with libejml-java v0.41.

- - - - -
20970603 by Andrius Merkys at 2022-11-24T02:40:29-05:00
Update changelog for 1.10.4+dfsg-5 release

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/patches/ignore_mac_install.patch
- debian/patches/update-ejml.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+beast-mcmc (1.10.4+dfsg-5) unstable; urgency=medium
+
+  * Team upload.
+  * Refresh ignore_mac_install.patch.
+  * Adjust update-ejml.patch to build with libejml-java 0.41.
+
+ -- Andrius Merkys <merkys at debian.org>  Thu, 24 Nov 2022 02:40:16 -0500
+
 beast-mcmc (1.10.4+dfsg-4) unstable; urgency=medium
 
   * Fix watch file


=====================================
debian/control
=====================================
@@ -22,7 +22,7 @@ Build-Depends: debhelper-compat (= 13),
                junit4,
                libmtj-java,
                libitext1-java,
-               libejml-java (>= 0.38),
+               libejml-java (>= 0.41),
                libjlapack-java
 Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/beast-mcmc


=====================================
debian/patches/ignore_mac_install.patch
=====================================
@@ -4,7 +4,7 @@ Last-Update: Tue, 16 Oct 2018 20:54:48 +0200
 
 --- a/build.xml
 +++ b/build.xml
-@@ -816,6 +816,6 @@
+@@ -820,6 +820,6 @@
          <echo message="Mac version release is finished."/>
      </target>
  


=====================================
debian/patches/update-ejml.patch
=====================================
@@ -1,5 +1,5 @@
 Author: Andrius Merkys <merkys at debian.org>
-Description: Migrating to libejml-java v0.38.
+Description: Migrating to libejml-java v0.41.
 --- a/src/dr/evomodel/treedatalikelihood/continuous/cdi/ContinuousDiffusionIntegrator.java
 +++ b/src/dr/evomodel/treedatalikelihood/continuous/cdi/ContinuousDiffusionIntegrator.java
 @@ -413,7 +413,7 @@
@@ -343,9 +343,10 @@ Description: Migrating to libejml-java v0.38.
              {
 -                final DenseMatrix64F Vtmp = new DenseMatrix64F(dimTrait, dimTrait);
 -                CommonOps.mult(Vd, Vprior, Vtmp);
+-                Vprior.set(Vtmp);
 +                final DMatrixRMaj Vtmp = new DMatrixRMaj(dimTrait, dimTrait);
 +                CommonOps_DDRM.mult(Vd, Vprior, Vtmp);
-                 Vprior.set(Vtmp);
++                Vprior.setTo(Vtmp);
              }
  
 -            final DenseMatrix64F Vtotal = new DenseMatrix64F(dimTrait, dimTrait);
@@ -735,21 +736,15 @@ Description: Migrating to libejml-java v0.38.
  
 -                final DenseMatrix64F Ptmp = new DenseMatrix64F(dimTrait, dimTrait);
 -                CommonOps.mult(Pd, Pprior, Ptmp);
-+                final DMatrixRMaj Ptmp = new DMatrixRMaj(dimTrait, dimTrait);
-+                CommonOps_DDRM.mult(Pd, Pprior, Ptmp);
-                 Pprior.set(Ptmp); // TODO What does this do?
-             }
- 
+-                Pprior.set(Ptmp); // TODO What does this do?
+-            }
+-
 -            final DenseMatrix64F Vtotal = new DenseMatrix64F(dimTrait, dimTrait);
 -//            CommonOps.add(Vroot, Vprior, Vtotal);
-+            final DMatrixRMaj Vtotal = new DMatrixRMaj(dimTrait, dimTrait);
-+//            CommonOps_DDRM.add(Vroot, Vprior, Vtotal);
- 
+-
 -            final DenseMatrix64F Ptotal = new DenseMatrix64F(dimTrait, dimTrait);
 -            CommonOps.invert(Vtotal, Ptotal);  // TODO Can return determinant at same time to avoid extra QR decomp
-+            final DMatrixRMaj Ptotal = new DMatrixRMaj(dimTrait, dimTrait);
-+            CommonOps_DDRM.invert(Vtotal, Ptotal);  // TODO Can return determinant at same time to avoid extra QR decomp
- 
+-
 -            final DenseMatrix64F tmp1 = new DenseMatrix64F(dimTrait, dimTrait);
 -            final DenseMatrix64F tmp2 = new DenseMatrix64F(dimTrait, dimTrait);
 -            CommonOps.add(Proot, Pprior, Ptotal);
@@ -757,6 +752,17 @@ Description: Migrating to libejml-java v0.38.
 -            CommonOps.mult(Vtotal, Proot, tmp1);
 -            CommonOps.mult(Proot, tmp1, tmp2);
 -            CommonOps.add(Proot, -1.0, tmp2, Ptotal);
++                final DMatrixRMaj Ptmp = new DMatrixRMaj(dimTrait, dimTrait);
++                CommonOps_DDRM.mult(Pd, Pprior, Ptmp);
++                Pprior.setTo(Ptmp); // TODO What does this do?
++            }
++
++            final DMatrixRMaj Vtotal = new DMatrixRMaj(dimTrait, dimTrait);
++//            CommonOps_DDRM.add(Vroot, Vprior, Vtotal);
++
++            final DMatrixRMaj Ptotal = new DMatrixRMaj(dimTrait, dimTrait);
++            CommonOps_DDRM.invert(Vtotal, Ptotal);  // TODO Can return determinant at same time to avoid extra QR decomp
++
 +            final DMatrixRMaj tmp1 = new DMatrixRMaj(dimTrait, dimTrait);
 +            final DMatrixRMaj tmp2 = new DMatrixRMaj(dimTrait, dimTrait);
 +            CommonOps_DDRM.add(Proot, Pprior, Ptotal);



View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/8e437309c182a09066bd8dc14f5797b840322d01...20970603692c84010c4d51c171f598eb77ca56de

-- 
View it on GitLab: https://salsa.debian.org/med-team/beast-mcmc/-/compare/8e437309c182a09066bd8dc14f5797b840322d01...20970603692c84010c4d51c171f598eb77ca56de
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