Move Copasi Optimization Solver to Client

Instead of the copasi optimization solver being within core, its now within client.
virtualcell · Jan 16, 2025 · 98a9930 · 98a9930
1 parent ea01c8d
commit 98a9930
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Showing 5 changed files with 12 additions and 7 deletions.
diff --git a/...ptimization/CopasiOptimizationSolver.java → ...java/copasi/CopasiOptimizationSolver.java b/...ptimization/CopasiOptimizationSolver.java → ...java/copasi/CopasiOptimizationSolver.java
@@ -8,7 +8,7 @@
  *  http://www.opensource.org/licenses/mit-license.php
  */
 
-package org.vcell.optimization;
+package copasi;
 
 import cbit.vcell.client.server.ClientServerInfo;
 import cbit.vcell.modelopt.ParameterEstimationTask;
@@ -20,6 +20,9 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.api.client.VCellApiClient;
+import org.vcell.optimization.CopasiOptSolverCallbacks;
+import org.vcell.optimization.CopasiUtils;
+import org.vcell.optimization.ParameterEstimationTaskSimulatorIDA;
 import org.vcell.optimization.jtd.*;
 import org.vcell.util.ClientTaskStatusSupport;
 import org.vcell.util.UserCancelException;

diff --git a/...t/vcell/modelopt/OptimizationService.java → .../copasi/modelopt/OptimizationService.java b/...t/vcell/modelopt/OptimizationService.java → .../copasi/modelopt/OptimizationService.java
@@ -1,8 +1,8 @@
-package cbit.vcell.modelopt;
+package copasi.modelopt;
 
+import cbit.vcell.modelopt.ParameterEstimationTask;
 import org.vcell.optimization.CopasiOptSolverCallbacks;
-import org.vcell.optimization.CopasiOptimizationSolver;
-import org.vcell.optimization.ParameterEstimationTaskSimulatorIDA;
+import copasi.CopasiOptimizationSolver;
 import org.vcell.util.Issue;
 import org.vcell.util.IssueContext;
 

diff --git a/...bit/vcell/modelopt/ProfileLikelihood.java → ...va/copasi/modelopt/ProfileLikelihood.java b/...bit/vcell/modelopt/ProfileLikelihood.java → ...va/copasi/modelopt/ProfileLikelihood.java
@@ -1,4 +1,4 @@
-package cbit.vcell.modelopt;
+package copasi.modelopt;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -8,6 +8,7 @@
 import cbit.vcell.mapping.MappingException;
 import cbit.vcell.mapping.SimulationContext;
 import cbit.vcell.math.MathException;
+import cbit.vcell.modelopt.*;
 import cbit.vcell.opt.OptSolverResultSet;
 import cbit.vcell.opt.OptSolverResultSet.OptRunResultSet;
 import cbit.vcell.opt.OptimizationResultSet;

diff --git a/vcell-client/src/main/java/org/vcell/optimization/gui/ParameterEstimationRunTaskPanel.java b/vcell-client/src/main/java/org/vcell/optimization/gui/ParameterEstimationRunTaskPanel.java
@@ -46,7 +46,7 @@
 import org.vcell.client.logicalwindow.LWContainerHandle;
 import org.vcell.client.logicalwindow.LWNamespace;
 import org.vcell.optimization.CopasiOptSolverCallbacks;
-import org.vcell.optimization.CopasiOptimizationSolver;
+import copasi.CopasiOptimizationSolver;
 import org.vcell.optimization.CopasiUtils;
 import org.vcell.optimization.ParameterEstimationTaskSimulatorIDA;
 import org.vcell.optimization.jtd.OptProgressItem;

diff --git a/...ization/CopasiOptimizationSolverTest.java → .../copasi/CopasiOptimizationSolverTest.java b/...ization/CopasiOptimizationSolverTest.java → .../copasi/CopasiOptimizationSolverTest.java
@@ -1,4 +1,4 @@
-package org.vcell.optimization;
+package copasi;
 
 import cbit.vcell.biomodel.BioModel;
 import cbit.vcell.mapping.MappingException;
@@ -15,6 +15,7 @@
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
+import org.vcell.optimization.CopasiUtils;
 import org.vcell.optimization.jtd.OptProblem;
 import org.vcell.optimization.jtd.Vcellopt;
 import org.vcell.util.ClientTaskStatusSupport;