Merge for release.

bd2kccd · May 19, 2023 · 81bb555 · 81bb555
2 parents 15439bf + d63bac4
commit 81bb555
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Showing 3 changed files with 7 additions and 25 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.8.0</version>
+    <version>1.9.0</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -22,7 +22,7 @@
         <dependency>
             <groupId>io.github.cmu-phil</groupId>
             <artifactId>tetrad-lib</artifactId>
-            <version>7.3.4</version>
+            <version>7.4.0</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java
@@ -34,9 +34,9 @@
 import edu.cmu.tetrad.graph.GraphUtils;
 import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetrad.graph.NodeType;
-import edu.cmu.tetrad.search.DagToPag;
-import edu.cmu.tetrad.search.SearchGraphUtils;
-import edu.cmu.tetrad.search.TsDagToPag;
+import edu.cmu.tetrad.search.utils.DagToPag;
+import edu.cmu.tetrad.search.utils.GraphSearchUtils;
+import edu.cmu.tetrad.search.utils.TsDagToPag;
 import edu.cmu.tetrad.util.Parameters;
 import edu.pitt.dbmi.causal.cmd.AlgorithmRunException;
 import edu.pitt.dbmi.causal.cmd.CmdArgs;
@@ -236,15 +236,15 @@ private Graph manipulateGraph(Graph graph) {
 
         if (cmdArgs.isChooseMagInPag()) {
             try {
-                graph = SearchGraphUtils.pagToMag(graph);
+                graph = GraphSearchUtils.pagToMag(graph);
             } catch (Exception exception) {
                 LOGGER.error("Unable to choose MAG in PAG.", exception);
             }
         }
 
         if (cmdArgs.isGeneratePatternFromDag()) {
             try {
-                graph = SearchGraphUtils.cpdagFromDag(graph);
+                graph = GraphSearchUtils.cpdagFromDag(graph);
             } catch (Exception exception) {
                 LOGGER.error("Unable to generate pattern graph from DAG.", exception);
             }

diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
@@ -87,24 +87,6 @@ public void testGFCIWithContinuousDataAndChooseMagInPag() throws Exception {
         CausalCmdApplication.main(args);
     }
 
-    @Test
-    public void testFaskVoteWithMultipleContinuousData() throws Exception {
-        String dataset1 = TestFiles.CONTINUOUS_DATA_20K_PART1;
-        String dataset2 = TestFiles.CONTINUOUS_DATA_20K_PART2;
-        String dirOut = TestFiles.createSubDir(tempDir, "fask-vote_cont").toString();
-        String[] args = {
-            "--dataset", dataset1 + "," + dataset2,
-            "--delimiter", "tab",
-            "--data-type", "continuous",
-            "--algorithm", "fask-vote",
-            "--test", "fisher-z-test",
-            "--score", "sem-bic-score",
-            "--default",
-            "--out", dirOut
-        };
-        CausalCmdApplication.main(args);
-    }
-
     @Test
     public void testGFCIWithContinuousDataAndVariablesToExclude() throws Exception {
         String dataset = TestFiles.CONTINUOUS_DATA;