Merge pull request #82 from bd2kccd/development

Update to Tetrad 7.1.3-1

README.md

@@ -3,3 +3,7 @@
 ## Introduction
 
 Causal-cmd is a Java application that provides a Command-Line Interface (CLI) tool for causal discovery algorithms produced by the [Center for Causal Discovery](http://www.ccd.pitt.edu/).  The documentation can be found here [https://bd2kccd.github.io/docs/causal-cmd/](https://bd2kccd.github.io/docs/causal-cmd/) 
+
+Public builds are available here:
+
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/causal-cmd/

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.4.2</version>
+    <version>1.5.0</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -21,7 +21,7 @@
         <dependency>
             <groupId>io.github.cmu-phil</groupId>
             <artifactId>tetrad-lib</artifactId>
-            <version>7.1.2-2</version>
+            <version>7.1.3-1</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -45,7 +45,7 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-engine</artifactId>
-            <version>5.9.1</version>
+            <version>5.9.2</version>
             <scope>test</scope>
         </dependency>
     </dependencies>

src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java

@@ -22,7 +22,7 @@
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.data.DataUtils;
 import edu.cmu.tetrad.data.DelimiterType;
-import edu.cmu.tetrad.data.IKnowledge;
+import edu.cmu.tetrad.data.Knowledge;
 import edu.cmu.tetrad.util.DataConvertUtils;
 import edu.pitt.dbmi.causal.cmd.AlgorithmRunException;
 import edu.pitt.dbmi.causal.cmd.CmdArgs;
@@ -99,13 +99,13 @@ public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws I
      * @return knowledge information from file
      * @throws IOException when errors occur during reading file
      */
-    public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throws IOException {
+    public static Knowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getKnowledgeFile();
         if (file == null) {
             return null;
         } else {
             LogMessages.readingFileStart(file, LOGGER, out);
-            IKnowledge knowledge = DataUtils.loadKnowledge(file.toFile(), DelimiterType.WHITESPACE, "//");
+            Knowledge knowledge = DataUtils.loadKnowledge(file.toFile(), DelimiterType.WHITESPACE, "//");
             LogMessages.readingFileEnd(file, LOGGER, out);
 
             return knowledge;

src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java

@@ -26,7 +26,7 @@
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.DataSet;
 import edu.cmu.tetrad.data.ICovarianceMatrix;
-import edu.cmu.tetrad.data.IKnowledge;
+import edu.cmu.tetrad.data.Knowledge;
 import edu.cmu.tetrad.graph.Dag;
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.graph.GraphUtils;
@@ -87,7 +87,7 @@ public TetradRunner(CmdArgs cmdArgs) {
     public void runAlgorithm(PrintStream out) throws AlgorithmRunException, IOException {
         final List<DataModel> dataModels = DataFiles.readInDatasets(cmdArgs, out);
         final Algorithm algorithm = getAlgorithm(cmdArgs);
-        final IKnowledge knowledge = DataFiles.readInKnowledge(cmdArgs, out);
+        final Knowledge knowledge = DataFiles.readInKnowledge(cmdArgs, out);
 
         final boolean acceptsKnowledge = TetradAlgorithms.getInstance().acceptKnowledge(cmdArgs.getAlgorithmClass());
         final boolean hasKnowledge = !(knowledge == null || knowledge.getVariables().isEmpty());

src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationBootstrappingTest.java

@@ -0,0 +1,57 @@
+/*
+ * Copyright (C) 2019 University of Pittsburgh.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ */
+package edu.pitt.dbmi.causal.cmd;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+/**
+ *
+ * Jan 13, 2023 12:16:29 AM
+ *
+ * @author Kevin V. Bui ([email protected])
+ */
+public class CausalCmdApplicationBootstrappingTest {
+
+    @TempDir
+    public static Path tempDir;
+
+    @Test
+    public void testFgesBootstrappingWithContinuousData() throws IOException {
+        String dataset = TestFiles.CONTINUOUS_DATA;
+        String dirOut = TestFiles.createSubDir(tempDir, "fges_bootstrapping").toString();
+        String[] args = {
+            "--dataset", dataset,
+            "--delimiter", "tab",
+            "--data-type", "continuous",
+            "--algorithm", "fges",
+            "--score", "ebic-score",
+            "--default",
+            "--prefix", "fges-bootstrapping",
+            "--numberResampling", "10",
+            "--percentResampleSize", "100",
+            "--seed", "1673588774198",
+            "--out", dirOut
+        };
+        CausalCmdApplication.main(args);
+    }
+
+}

src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationExperimentalTest.java

@@ -0,0 +1,56 @@
+/*
+ * Copyright (C) 2019 University of Pittsburgh.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ */
+package edu.pitt.dbmi.causal.cmd;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+/**
+ *
+ * Jan 21, 2023 9:52:10 PM
+ *
+ * @author Kevin V. Bui ([email protected])
+ */
+public class CausalCmdApplicationExperimentalTest {
+
+    @TempDir
+    public static Path tempDir;
+
+    @Test
+    public void testBossWithContinuousData() throws IOException {
+        String dataset = TestFiles.CONTINUOUS_DATA;
+        String dirOut = TestFiles.createSubDir(tempDir, "boss_experimental").toString();
+        String[] args = {
+            "--dataset", dataset,
+            "--delimiter", "tab",
+            "--data-type", "continuous",
+            "--experimental",
+            "--algorithm", "boss",
+            "--score", "ebic-score",
+            "--test", "fisher-z-test",
+            "--default",
+            "--prefix", "boss-experimental",
+            "--out", dirOut
+        };
+        CausalCmdApplication.main(args);
+    }
+
+}